Abstract

Motivation: Prokaryotic genomes are sequenced and annotated at an increasing rate. The methods of annotation vary between sequencing groups. It makes genome comparison difficult and may lead to propagation of errors when questionable assignments are adapted from one genome to another. Genome comparison either on a large or small scale would be facilitated by using a single standard for annotation, which incorporates a transparency of why an open reading frame (ORF) is considered to be a gene.

Results: A total of 143 prokaryotic genomes were scored with an updated version of the prokaryotic genefinder EasyGene. Comparison of the GenBank and RefSeq annotations with the EasyGene predictions reveals that in some genomes up to ∼60% of the genes may have been annotated with a wrong start codon, especially in the GC-rich genomes. The fractional difference between annotated and predicted confirms that too many short genes are annotated in numerous organisms. Furthermore, genes might be missing in the annotation of some of the genomes. We predict 41 of 143 genomes to be over-annotated by >5%, meaning that too many ORFs are annotated as genes. We also predict that 12 of 143 genomes are under-annotated. These results are based on the difference between the number of annotated genes not found by EasyGene and the number of predicted genes that are not annotated in GenBank.

We argue that the average performance of our standardized and fully automated method is slightly better than the annotation.

Availability: The EasyGene 1.2 predictions and statistics can be accessed at

Contact:pern@binf.ku.dk

INTRODUCTION

Hundreds of prokaryotic genomes have been sequenced. This has completely changed microbial research and facilitated large-scale comparative genomics. The annotation process often includes a lot of meticulous inspection done by experts, whose detailed biological knowledge is very valuable for this work. Unfortunately, the annotation quality of the genomes varies a lot and it makes comparisons difficult. Various sequencing groups use different tools for annotation, and the varying criteria for when to annotate an open reading frame (ORF) as a gene makes the annotation very uneven. It may in some cases lead to erroneous assignments of name and function, or to over-annotation when an assignment is adapted to other genomes. It is well known that many public databases contain such erroneous data and that the errors have a tendency to propagate (Doerks et al., 1998; Galperin and Koonin, 1998). This will become an even bigger problem than it is today as the rate of genome sequencing and annotation will keep increasing. A general standard for annotation would help to prevent this from happening and facilitate genome comparison.

Automated methods for prokaryotic genefinding like GLIMMER (Salzberg et al., 1998; Delcher et al., 1999; ), ORPHEUS (Frishman et al., 1998) and different versions of GeneMark (Lukashin and Borodovsky, 1998; Besemer and Borodovsky, 1999; Besemer et al., 2001) have been widely used in genome sequencing projects [see for instance (Fitz-Gibbon et al., 2002; Cerdeno-Tarraga et al., 2003; Wei et al., 2003; McLeod et al., 2004)]. GLIMMER uses interpolated Markov models whose predictions are based on oligomers of varying length and on local sequence composition (Salzberg et al., 1998; Delcher et al., 1999). ORPHEUS utilizes similarity derived genes to create codon usage and ribosome binding site statistics, which are used to predict additional genes (Frishman et al., 1998). GeneMark.hmm uses a hidden Markov model (HMM) framework whose initial parameters are predetermined from the statistics of annotated genes. In post-processing evaluation of ribosome binding sites is applied (Lukashin and Borodovsky, 1998). Later a heuristic approach for model derivation was implemented (Besemer and Borodovsky, 1999) and in GeneMarkS an iterative training procedure is added (Besemer et al., 2001).

Here we present a resource of fully automated and homogeneous annotation of protein coding genes in the publicly available genomes. It is based on an updated version of the prokaryotic genefinder EasyGene (Larsen and Krogh, 2003). The most important difference between EasyGene and other genefinders is the use of a statistical significance measure. EasyGene takes a genome sequence as input and gives a list of statistically significant genes as output. In comparison with the abovementioned genefinders, EasyGene is generally better at predicting the exact gene starts and has a very good combined sensitivity/specificity performance for both AT-rich and GC-rich genomes. Furthermore, the results of 10-fold cross-validation sensitivity indicate that EasyGene avoids over-fitting (Larsen and Krogh, 2003).

The aim is to create a homogeneous resource of gene predictions and other available information from Easygene 1.2 for all the prokaryotic genomes made public. Our objective is to present the information in a clear and easily comprehensible way and to facilitate cross-referencing to other data. We believe that this will be a valuable resource for genome comparison and hope that it is a step towards a more standardized annotation.

Statistics is provided on GenBank and RefSeq annotations as well as on the EasyGene predictions for each genome. The results indicate that wrong start codons and over-annotation of short genes pose the major problems in prokaryotic genome annotations. Furthermore, it seems that the fully automated predictions on average are more reliable than the annotation, although such a claim is difficult to prove.

METHODS

EasyGene is based on an HMM whose parameters are genome specific. The training sets for parameter estimation are made by extracting all maximal ORFs with a length above 120 bases and translating them into proteins. The Swiss-Prot database (Boeckmann et al., 2003) is searched for significant matches to the proteins using ungapped BLASTP (Altschul et al., 1990) and an E value of 10−5. Hits to the query genus are discarded. Proteins with certain keywords (see below) are also removed. The ORFs with significant hits are processed into two sequence sets. One set contains all of these ORFs, which are considered to be certain genes. The other set contains certain genes with only one possible start codon (Frishman et al., 1998). Both sets are similarity reduced (Hobohm et al., 1992) and used for training of an HMM. The putative genes in the genome are then scored with the HMM and a measure of the statistical significance is calculated (R). R is the expected number of ORFs that may be predicted with the same length-adjusted score or better in one megabase of random DNA with the same third order Markov statistics as the genome. For each ORF length, the score is adjusted such that the expected number of predictions is constant. For more details see Larsen and Krogh (2003).

In the following section this paper defines ‘certain genes with certain start’ to be the maximal ORFs that have significant matches to Swiss-Prot in a BLASTP search, and where the hits are distributed in such a manner that only the most upstream start codon can be the start of the gene. The set of ‘certain genes with uncertain start’ denotes the ORFs whose matches leave more than one possible start of the gene. We consider all the ‘certain genes’ to be real genes as they have significant matches to Swiss-Prot (Frishman et al., 1998; Larsen and Krogh, 2003).

We have analysed 143 publicly available prokaryotic genomes with EasyGene 1.2 and present the predictions on the EasyGene 1.2 webpage.

For each genome the results are presented in four formats.

(1) GFF. It contains a header with genome name and identifier, model version, creation date, R cutoff, version of Swiss-Prot used in the BLASTP search and the genus from which proteins were excluded from the training set. The official GFF format contains eight mandatory and two optional fields (). To meet our purpose the optional commentary field has been subdivided into six columns (Fig. 1).

Fig. 1

The predictions for each sequence are presented on a separate page. The pages provide for easy access to the sequence of predicted CDSs and facilitate navigation to the relevant BLASTP report, Swiss-Prot data and NCBI resources. Each column is described in links on the page. The first eight columns comply with the GFF format. Columns 9–14 are an extension of the GFF commentary field. These columns contain information about the maximal ORF, the predicted start codon, the sequence log-odds score, the type of sequence, the highest scoring match in Swiss-Prot and the match to GenBank and RefSeq annotation. For further description, see the webpage.

Fig. 1

The predictions for each sequence are presented on a separate page. The pages provide for easy access to the sequence of predicted CDSs and facilitate navigation to the relevant BLASTP report, Swiss-Prot data and NCBI resources. Each column is described in links on the page. The first eight columns comply with the GFF format. Columns 9–14 are an extension of the GFF commentary field. These columns contain information about the maximal ORF, the predicted start codon, the sequence log-odds score, the type of sequence, the highest scoring match in Swiss-Prot and the match to GenBank and RefSeq annotation. For further description, see the webpage.

(2) HTML. The HTML version of the GFF page is augmented with links to other information. For each prediction there are links to the BLASTP reports, predicted CDS sequences (in FASTA format), Swiss-Prot and GenBank. If the annotations differ, links to both are given. RefSeq annotation is written in parentheses. Furthermore, all predicted CDSs can be downloaded from this page (Fig. 1).

(3) NARROW HTML. It is similar to the HTML version but without columns 1, 2 and 8 (for columns see Fig. 1).

(4) CDS. It contains the same header as the GFF version and all the predicted CDSs for the organism in FASTA format.

The GenBank files for 25 of the genomes contain CDSs with the label ‘/pseudo’, which means that the CDS is considered to be a pseudogene by the annotators. These are the pseudogenes we include in column 9.6 and in the subsequent analysis of our results.

A statistical evaluation of the output from EasyGene 1.2 and information for each of the 143 genomes are collected in three tables. Table 1 contains general information about the genomes as well as the annotation and the predictions. Table 2 focuses on the differences between the annotation and the predictions. Table 3 compares the annotation and the predictions with the certain genes (see Tables 1, 3 and 4 for examples). The full tables are used for comparative analysis of the genomes and are available on the EasyGene 1.2 webpage.

Table 1

Example of statistics in Table 1 of the EasyGene 1.2 output obtained for nine organisms using R-value cutoff = 2

Genome G size AT GBc GFc 
Aeropyrum pernix 2694 (1841) 1695 1 669 695 43.7 77.3 (85.4) 88.1 
Rickettsia conorii Malish1374 (1374) 1183 1 268 755 67.6 80.5 (80.5) 75.8 
Xylella fastidiosa 9a5c 2766 (2766) 2366 2 679 306 47.3 83.2 (83.2) 76.0 
Vibrio cholerae chr. II 1091 (1092) 919 1 072 315 53.1 84.4 (84.5) 82.2 
Leptospira interrogans chr. I 4358 (4360) 3206 4 332 241 65 77.9 (77.9) 73.4 
L.interrogans chr. II 367 (367) 284 358 943 64.9 79.6 (79.6) 75.6 
Pirellula sp. 7322 (7322) 4788 7 145 576 44.6 94.6 (94.6) 84.7 
Clostridium tetani E88 2372 (2372) 2733 2 799 251 71.3 85.4 (85.4) 86.9 
Bordetella pertussis 3805 (3806) 4172 4 086 189 32.3 82.7 (82.7) 88.5 
Genome G size AT GBc GFc 
Aeropyrum pernix 2694 (1841) 1695 1 669 695 43.7 77.3 (85.4) 88.1 
Rickettsia conorii Malish1374 (1374) 1183 1 268 755 67.6 80.5 (80.5) 75.8 
Xylella fastidiosa 9a5c 2766 (2766) 2366 2 679 306 47.3 83.2 (83.2) 76.0 
Vibrio cholerae chr. II 1091 (1092) 919 1 072 315 53.1 84.4 (84.5) 82.2 
Leptospira interrogans chr. I 4358 (4360) 3206 4 332 241 65 77.9 (77.9) 73.4 
L.interrogans chr. II 367 (367) 284 358 943 64.9 79.6 (79.6) 75.6 
Pirellula sp. 7322 (7322) 4788 7 145 576 44.6 94.6 (94.6) 84.7 
Clostridium tetani E88 2372 (2372) 2733 2 799 251 71.3 85.4 (85.4) 86.9 
Bordetella pertussis 3805 (3806) 4172 4 086 189 32.3 82.7 (82.7) 88.5 

A, number of annotated genes including CDSs labelled as pseudogenes; P, number of predicted genes; G size, genome size; AT, AT content in percent; GBc, coding percentage of genome as annotated in GenBank not including pseudogenes; GFc, coding percentage of genome as predicted by EasyGene. Values for the annotation are given for GenBank and (RefSeq).

Table 2

Proteins are removed if they have one of these keywords

Alternative initiation Possible 
Bacteriophage Probable 
Hypothetical Putative 
Hypothetical protein Transposable element 
Insertion Transposon 
Phage Unknown 
Phagocytosis Viral occlusion body 
Plasmid Virulence 
Alternative initiation Possible 
Bacteriophage Probable 
Hypothetical Putative 
Hypothetical protein Transposable element 
Insertion Transposon 
Phage Unknown 
Phagocytosis Viral occlusion body 
Plasmid Virulence 
Table 3

Examples from Table 2 of the EasyGene 1.2 output

Genome AeP AnP PnA DS Ap ApE 
A.pernix 1567 (1563) 1127 (278) 128 (132) 1001 (977) 0 (0) 0 (0) 
R.conorii Malish1149 (1149) 225 (225) 34 (34) 160 (160) 0 (0) 0 (0) 
X.fastidiosa 9a5c 2043 (2043) 723 (723) 323 (323) 783 (783) 0 (0) 0 (0) 
V.cholerae chr. II 880 (881) 211 (211) 39 (38) 298 (298) 0 (0) 0 (0) 
L.interrogans chr. I 3168 (3168) 1190 (1192) 38 (38) 820 (820) 0 (0) 0 (0) 
L.interrogans chr. II 282 (282) 85 (85) 3 (3) 83 (83) 0 (0) 0 (0) 
Pirellula sp. 4728 (4728) 2594 (2594) 60 (60) 2314 (2314) 0 (0) 0 (0) 
C.tetani E88 2347 (2347) 26 (26) 386 (386) 734 (734) 0 (0) 0 (0) 
B.pertussis 3695 (3695) 110 (111) 477 (477) 1329 (1329) 359 (359) 281 (281) 
Genome AeP AnP PnA DS Ap ApE 
A.pernix 1567 (1563) 1127 (278) 128 (132) 1001 (977) 0 (0) 0 (0) 
R.conorii Malish1149 (1149) 225 (225) 34 (34) 160 (160) 0 (0) 0 (0) 
X.fastidiosa 9a5c 2043 (2043) 723 (723) 323 (323) 783 (783) 0 (0) 0 (0) 
V.cholerae chr. II 880 (881) 211 (211) 39 (38) 298 (298) 0 (0) 0 (0) 
L.interrogans chr. I 3168 (3168) 1190 (1192) 38 (38) 820 (820) 0 (0) 0 (0) 
L.interrogans chr. II 282 (282) 85 (85) 3 (3) 83 (83) 0 (0) 0 (0) 
Pirellula sp. 4728 (4728) 2594 (2594) 60 (60) 2314 (2314) 0 (0) 0 (0) 
C.tetani E88 2347 (2347) 26 (26) 386 (386) 734 (734) 0 (0) 0 (0) 
B.pertussis 3695 (3695) 110 (111) 477 (477) 1329 (1329) 359 (359) 281 (281) 

AeP, number of annotated genes that are predicted (identical stop codons) including CDSs labelled as pseudogenes; AnP, number of genes annotated but not predicted including pseudogenes; PnA, number of genes predicted but not annotated; DS, number of genes from AeP annotated with a different start than predicted; Ap, CDSs annotated as pseudogenes; ApE, CDSs annotated as pseudogenes and predicted to be real genes. Values for the annotation are given for GenBank and (RefSeq).

Table 4

Examples from Table 3 of the EasyGene 1.2 output

Genome CnA CnP CS CSADS CSPDS 
A.pernix 736 5 (9) 203 72 (68) 
R.conorii Malish656 9 (9) 20 426 1 (1) 
X.fastidiosa 9a5c 2475 27 (27) 29 699 16 (16) 24 
V.cholerae chr. II 2317 25 (25) 857 1 (7) 
L.interrogans chr. I 1578 3 (3) 15 706 20 (20) 20 
L.interrogans chr. II 1578 1 (1) 706 5 (5) 
Pirellula sp. 2041 9 (9) 37 413 8 (8) 36 
C.tetani E88 1485 83 (83) 661 16 (16) 
B.pertussis 2345 100 (100) 12 654 82 (82) 96 
Genome CnA CnP CS CSADS CSPDS 
A.pernix 736 5 (9) 203 72 (68) 
R.conorii Malish656 9 (9) 20 426 1 (1) 
X.fastidiosa 9a5c 2475 27 (27) 29 699 16 (16) 24 
V.cholerae chr. II 2317 25 (25) 857 1 (7) 
L.interrogans chr. I 1578 3 (3) 15 706 20 (20) 20 
L.interrogans chr. II 1578 1 (1) 706 5 (5) 
Pirellula sp. 2041 9 (9) 37 413 8 (8) 36 
C.tetani E88 1485 83 (83) 661 16 (16) 
B.pertussis 2345 100 (100) 12 654 82 (82) 96 

C, number of certain genes (possibly with unknown start); CnA, number of certain genes not annotated; CnP, number of certain genes not predicted; CS, number of certain genes with certain start in the training set; CSADS, CS annotated with a different start; CSPDS, CS predicted with a different start. The values for C and CS are model specific and will be the same for each sequence run by the same model. Values for the annotation are given for GenBank and (RefSeq).

In our comparisons we say that an annotated or a certain gene is predicted if the stop codons are identical. Separate statistics is done on the correspondence of start codons.

Modifications to EasyGene

For the present work several adjustments have been made to the original EasyGene implementation. The most important alteration from the user's point of view is the prediction of alternative starts.

Training on multiple genomes or on separate parts from one genome is now possible. This is an advantage if proteins from plasmids are to be included in the training set or in cases where no whole-genome file exists.

A low-complexity filtered (Wootton and Federhen, 1993) version of the Swiss-Prot database is used in the BLAST search to avoid that local amino acid over-representation in the query results in high scoring matches in low-complexity regions.

The content of the ID line in the FASTA version of Swiss-Prot is changed in order to control the information available for further processing. Once a BLAST report is created [see Larsen and Krogh (2003) for details], proteins are eliminated from further processing if they come from organisms with the same genus as that of the query-genome. Proteins are also removed if they belong to the superkingdom ‘Viruses’ or if they have one of the keywords in Table 2. In the original version of EasyGene a shorter list of keywords was used to exclude proteins based on the ID line written in the BLAST report. The ID line was copied from the Swiss-Prot description line. This was not an optimal approach as the ID line becomes truncated in the BLAST report. Sometimes proteins were processed because the keyword appeared after the truncation. In Version 1.2 the list has been expanded to include words from the Swiss-Prot keyword line and the elimination is based on both the entire description line and the keyword line. We found it necessary to search both lines because they do not always correspond.

Additional alterations have been made such that proteins from other organisms can be rejected. For instance one might wish to exclude proteins from Salmonellas in a model for Escherichia coli K12 because of their close relationship.

The HMM implementation uses scaling of probabilities (Durbin et al., 1998). The drawback of this method is that for very long ORFs with a high probability of being a CDS, the relative probability of a non-coding state in the model drops below machine precision. This happens when the ratio of the coding to non-coding probability is of the order of 10600, which in practice means for some ORFs longer than ∼3000 bp. Therefore the probability of finding a subsequent coding region becomes zero. This underflow problem is dealt with by testing whether predictions are made both before and after all ORFs with a length of 3000 bases or more (lORF). The lORF has to be located more than 6000 bases from the sequence start or end. If the test fails, the entire sequence is split into segments, each matching an lORF or an intermediate region. Both types of segments are extended by 51 bases on either side as an attempt not to miss overlapping predictions at the edges. New predictions are made for each segment and subsequently combined into one output. If the test is passed, the original output is used for further processing.

The model gives a log-odds score for all possible starts of a gene. All start codons with a score that differs no more than 15 from the best is reported as alternative start positions. This number was chosen because it results in ∼1 alternative start codon being reported for each certain start gene, for the genomes Bordetella parapertussis (AT = 31.9%) and E.coli K12 (AT = 49.2%).

Programs have been made to add information to the EasyGene output about the difference between predictions and annotations. Information is also available about correspondence between prediction and certain genes and about Swiss-Prot matches.

From the final model output, webpages are created automatically and put on the EasyGene 1.2 homepage. The webpages contain the predictions and links to NCBI and Swiss-Prot.

We create three tables containing information and statistical evaluation of output data for each genome (see Tables 1, 3 and 4 for examples). The tables are also used to check for suspicious behaviour of EasyGene. If for instance the set of certain genes is poorly predicted for a particular genome, the predictions are inspected manually and a new model might be created.

RESULTS AND DISCUSSION

From the data of 143 prokaryotic genomes we observe that the fraction of certain genes with certain start (ORFs with significant Swiss-Prot matches and only one possible start codon) in the certain genes set increases with higher AT content (Fig. 2). These genes comprise more than half of the set when the AT content is >67.9%. This points to the difficulty of identifying the correct start codons in organisms with low AT content. In these organisms the G-rich start codon GTG is used much more frequently than in AT-rich organisms. Furthermore, in GC-rich organisms the frequency of GTG is higher than the frequency of stop codons (TAA, TGA, TAG). In the AT-rich organisms the frequency of start codons is the same or lower as that of the stop codons. Therefore, there are generally more possible start codons for each stop codon in GC-rich organisms.

Fig. 2

The fraction of certain start genes in the training set increases in genomes with higher AT content and is generally >50% when AT exceeds 67.6%.

Fig. 2

The fraction of certain start genes in the training set increases in genomes with higher AT content and is generally >50% when AT exceeds 67.6%.

EasyGene only considers the three most common start codons ATG, GTG and TTG. Prokaryotes can use five additional start codons and genes with these start codons will be predicted to have a wrong start. Furthermore, the set of certain genes with certain starts can potentially contain genes with the wrong start. This might bias the model to predict a wrong start codon even in the case where ATG, TTG or GTG is being used. However, ATG, GTG and TTG are considered to be the most abundant by far, and based on EasyGene's ability to predict experimentally verified start codons in E.coli (Larsen and Krogh, 2003), we believe the effects of excluding the alternative start codons to be minor.

In the following discussion we consider each sequence separately as it is annotated in GenBank, unless otherwise stated. The majority of plasmids and extra chromosomal elements are short sequences and do not have many genes compared to an entire genome. If the annotation and the predictions differ in a few genes, the fractional differences for each sequence become large and skew the general results. It is difficult to interpret these differences between annotation and prediction for plasmids and extra chromosomal elements and they are therefore omitted from the discussion. As expected, Figure 3 shows that there is an increasing tendency to both annotate (slope = 0.62) and predict (slope = 0.80) the most upstream start codon with higher AT content in a genome. However, in the annotations the most upstream start codon is generally preferred much more frequently than predicted by EasyGene, especially in genomes with AT content <50%. We also observe that the fraction of predicted genes with a different start codon than the annotated one is higher in GC-rich organisms (Fig. 4). The outliers Aeropyrum Pernix and Pirellula sp. are predicted to have 59.1 and 48.3% genes with a different start, respectively. We obviously do not know the true number of most upstream start codons being used. From the above discussion and the picture emerging from the EasyGene predictions, we believe there is a tendency to use the most upstream start codon too often in the annotations. There are of course well-annotated genomes with many experimentally validated starts where this discussion does not apply.

Fig. 3

There is a tendency towards annotating genes with the most upstream start codon. Particularly in GC-rich genomes this is done much more often than predicted by EasyGene.

Fig. 3

There is a tendency towards annotating genes with the most upstream start codon. Particularly in GC-rich genomes this is done much more often than predicted by EasyGene.

Fig. 4

The fraction of predicted genes with a start codon different from the annotated one is higher in genomes with low AT content. The largest differences are found in A.pernix and Pirellula sp. The fraction of annotated genes equal to predicted based on stop codon comparison increases with higher AT content.

Fig. 4

The fraction of predicted genes with a start codon different from the annotated one is higher in genomes with low AT content. The largest differences are found in A.pernix and Pirellula sp. The fraction of annotated genes equal to predicted based on stop codon comparison increases with higher AT content.

There is an increase (slope = 0.07) in the fraction of annotated genes that are predicted, with growing AT content (Fig. 4). Again, this indicates the difficulty in finding genes in GC-rich organisms. There are generally more annotated genes that are not predicted, than vice versa (data not shown).

Skovgaard et al. (2001) published a study of 33 microbial genomes, which indicated that the genomes were all over-annotated to a higher or lesser degree. Based on the predictions from EasyGene we wanted to investigate the over-annotation issue again, to see if the same trend applies to the larger number of available genomes. When comparing the genomic coding percentage predicted by EasyGene to the annotated value with regard to either genome size or AT content no clear trend can be seen. However, this may be due to EasyGene generally predicting longer genes, while there are many short genes annotated (Fig. 5). Skovgaard et al. (2001) showed that it is generally more difficult to discriminate between short genes and random ORFs in GC-rich organisms. We observe a tendency towards annotating a larger fraction of short genes in GC-rich organisms, which supports the previous study. To assess the over-annotation in terms of the difference between the number of annotated and predicted genes we need a single standard for comparison. We do not know the true number of genes in a genome. The genomes have been annotated by different methods which makes the total number of annotated genes unsuitable as a standard. Instead we use the total number of predicted genes. The over-annotation is defined as follows:  

(1)
over-annotation%=(#Annotated#Predicted)100#Predicted.

Fig. 5

In many genomes the fraction of small annotated genes is larger than the fraction of small predicted genes (most extreme in Pirellula sp., L.interrogans chr. I and II, and X.fastidiosa 9a5c). Fractions are with respect to all predicted genes. For a few genomes short genes could be missing from the annotation (e.g. C.tetani E88). EasyGene 1.2 generally predicts longer genes than what is annotated (B.pertussis).

Fig. 5

In many genomes the fraction of small annotated genes is larger than the fraction of small predicted genes (most extreme in Pirellula sp., L.interrogans chr. I and II, and X.fastidiosa 9a5c). Fractions are with respect to all predicted genes. For a few genomes short genes could be missing from the annotation (e.g. C.tetani E88). EasyGene 1.2 generally predicts longer genes than what is annotated (B.pertussis).

We do not include the annotated pseudogenes in this calculation. Using the difference between the number of annotated and predicted genes may lead to estimations that are too high or too low. However, based on a previous sensitivity study (Larsen and Krogh, 2003) we believe that the estimates are reasonable. We predict 41 of 143 organisms to be over-annotated by >5%. Especially Rickettsia conorii Malish 7 (16%), Xylella fastidiosa 9a5c (17%), Vibrio cholerae chromosome II (19%), Leptospira interrogans chromosome I (36%) and II (29%), Pirellula sp. (53%) and A.pernix (59%) seem to have many annotated CDSs that are not likely to be real genes. Common to them all is that a large fraction of the annotated proteins is short (Fig. 5), which is an indication of over-annotation (Skovgaard et al., 2001). When considering the RefSeq annotation for A.pernix the predicted over-annotation drops to 9% because many of the short genes annotated in GenBank have been removed.

Of 143 organisms 12 are predicted to be under-annotated by >5%. Of these Clostridium tetani E88 (13%) and Bordetella pertussis (17%) show the largest deviation. For C.tetani E88 EasyGene predicts a larger percentage of short genes (Fig. 5) than what is annotated, indicating that perhaps there are short genes missing in the annotation. In B.pertussis 78% of the annotated pseudogenes are predicted to be real, which would explain the predicted under-annotation and point to a possible problem for EasyGene in handling pseudogenes.

Of the genomes 26 contain CDSs that are labelled as pseudogenes in the annotation. The number of pseudogenes range from 1 (Tropheryma whippleii TW08) to 359 (B.pertussis). EasyGene predicts on average 53% of the pseudogenes in a genome to be real genes. Among the 12 genomes predicted to be under-annotated there are 3 organisms (B.pertussis, B.parapertussis and Nitrosomonas europaea) with more than 100 pseudogenes annotated and a large percentage of these are predicted to be real. Hence, EasyGene cannot distinguish some of the pseudogenes from real genes. This is not a problem for all genomes with many pseudogenes and we have no explanation why the abovementioned genomes stand out.

To assess the performance of EasyGene we consider the certain genes not predicted with an R-cutoff of 2 (default) for models based on one sequence only. The percentage of certain genes that are not predicted range from 0 to 8% (mean 1.3%). In comparison, the annotation misses 0–7% (mean = 1.6%) of the genes. This indicates that EasyGene is able to find real genes that are not annotated and that the average performance of EasyGene is a little better than that of the annotation. For the certain genes with certain start EasyGene predicts the wrong start for 0–15% (mean = 4.6%). We expect the annotation to be doing better than EasyGene in this measurement because the most upstream start, which is always correct in our set with certain starts, is often preferred in the annotations. Indeed we observe that 0–35% (mean = 4.4%) are considered to have a different start by the annotation. This does not indicate that the annotation of all the start codons is better on average. Experimentally validated annotations will of course outperform EasyGene.

Some prokaryotic genomes have regions that are known to be horizontally acquired and therefore may have different sequence statistics. To investigate EasyGenes ability to predict genes in such regions we have looked at predictions in some of the pathogenicity islands in E.coli O157:H7 and Salmonella typhimurium (Table 5). In E.coli O157:H7 the locus of enterocyte effacement (LEE) contains 54 ORFs (Perna et al., 1998). EasyGene finds 94% of the confirmed genes and all the confirmed start genes in this region. Of the 54 ORFs 91% are predicted to be genes. In S.typhimurium pathogenicity islands 1 (SPI1) and 4 (SPI4) there are 48 and 18 ORFs, respectively (Marcus et al., 2000). There are no confirmed start genes found in SPI4. EasyGene predicts all confirmed genes in these regions. Ninety-four percent and 55% of the ORFs are predicted to be genes in SPI1 and SPI4, respectively. It seems that EasyGene is able to find genes in horizontally transferred segments, at least in the examples mentioned here.

Table 5

Predictions in pathogenicity islands (PAI) in E.coli O157:H7 (LEE) and S.typhimurium (SPI1 and SPI4)

PAI CF CS CSF ORFs CDSs 
LEE 16 15 54 49 
SPI1 29 29 10 10 48 45 
SPI4 18 10 
PAI CF CS CSF ORFs CDSs 
LEE 16 15 54 49 
SPI1 29 29 10 10 48 45 
SPI4 18 10 

C, number of certain genes (possibly with unknown start) in the region; CF, number of certain genes found; CS, number of certain genes with certain start in the region; CSF, CS found; ORFs, number of ORFs in the region; CDSs, number of CDSs predicted in the region (R = 2).

It is possible that the ‘certain gene’ sets contain errors because of matches to wrong genes in Swiss-Prot, matches to low complexity regions that have escaped detection, or because of random matches.

By removing hits from closely related organisms, we limit the first problem at the cost of losing lineage-specific genes in the training set. This will only be a problem if the statistics of these genes differ from the rest of the genes. Perhaps the prediction of lineage-specific short genes are affected too.

Low complexity regions are masked both in the database and in the BLAST search, so we believe that this problem is minimal.

Finally, we have a reasonably stringent E-value cut-off (10−5), which should avoid random matches. We therefore believe that the number of wrong ‘certain genes’ is very small, and probably as small as one can hope for in a fully automated procedure.

CONCLUSION

We have shown that accurate annotation of prokaryotic genomes still is not an easy task to undertake and that problems with wrongly annotated protein coding genes seem to persist in many organisms. A major issue that needs attention is the discrimination between short random ORFs and real genes. This problem is the largest contributor to over-annotation, especially in GC-rich genomes. There is a tendency for annotators to choose the most upstream start codon for a gene and there are genomes where this has been done for >99% of the genes. This seems extreme, even though AT-rich organisms have fewer start codons per stop codon than GC-rich organisms. More transparency in the annotation process and in the presentation is needed for others to understand these choices.

On average our fully automated method performs slightly better than the manual annotation. Therefore, we believe that EasyGene can be used as a valuable time-saving tool in the annotation work flow. Combining a very good initial starting point and the biological knowledge of the annotators, which is difficult to incorporate in a fully automated method, could increase the time spent on the more challenging problems in prokaryotic genome annotation and increase the overall performance.

We have presented the gene predictions for 143 genomes made by EasyGene 1.2. These predictions are made using a single standard, which facilitates comparison of related genomes and large-scale studies like the current one. The predictions are available from our website along with the statistical tables used in this study. The website has easy access to related resources at NCBI and Swiss-Prot and will be updated with new genomes.

We thank Lars G. T. Joergensen, who has made a large contribution to the database and website, and Thomas Schou Larsen, Morten Lindow, Lise Petersen and Kasper Munch Terkelsen for valuable discussions. This work was supported by the Danish National Research Foundation and by EU grant no. QLRI-CT-2001-00015.

Conflict of Interest: none declared.

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