many genbank entries for complete microbial genomes ... · the genbank staff is ensuring that only...

Conference Paper

Many Genbank entries for completemicrobial genomes violate the Genbankstandard

Peter D. Karp*Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA

*Correspondence to:P. D. Karp, BioinformaticsResearch Group, SRI International,EK223, 333 RavenswoodAvenue, Menlo Park, CA 94025,USA.E-mail: [email protected]

Abstract

A survey of Genbank entries for complete microbial genomes reveals that the majority do

not conform to the Genbank standard. Typical deviations from the Genbank standard

include records with information in incorrect fields, addition of extraneous and confusing

information within a field, and omission of useful fields. This situation results from two

principal causes: genome centres do not submit Genbank records in the proper form and

the Genbank, EMBL and DDBJ staffs do not enforce the database standards that they

have defined. Copyright # 2001 John Wiley & Sons, Ltd.

Keywords: genome annotation; Genbank; bioinformatics; database standards

Introduction

Genome annotation is a complex process with anumber of phases including gene finding, predictionof gene function, prediction of pathways andsubmission of the genome to the Genbank/EMBL/DDBJ databases (henceforth referred to simply asGenbank). If a submitted genome is not preparedaccording to the Genbank standard, the scientificcommunity will face significant barriers in accessingand manipulating the genome annotation that wasso painstakingly produced. This article presentsevidence that many complete genomes withinGenbank were not prepared according to theGenbank standard.

Genbank now contains 30 complete bacterialgenomes. As the number of complete genomesincreases, it becomes more and more importantthat data within Genbank are encoded in aconsistent and regular form that allows computerprograms to reliably extract information, sincemanual interpretation of those records becomesless and less feasible. For example, a computerprogram that attempts to search across manydifferent Genbank entries to find a given codingregion by gene name, or by gene-product name, orby the unique identifier assigned by a sequencing

project, must know what Genbank feature-tablequalifiers to search for each of these types ofinformation. In isolation, none of the examplespresented are that dramatic but, taken together, thescale and diversity of these malformed data createsa significant barrier to computational analysis ofGenbank.

The Genbank standard is neitherfollowed nor enforced

The genome centres that have submitted Genbankentries for complete genomes are not following theGenbank standard (which is available at http://www.ncbi.nlm.nih.gov/collab/FT/index.html) and theNCBI, EMBL and DDBJ groups that accept newGenbank entries are not enforcing that standard.Figure 1 shows excerpts from three Genbank entriesfor complete microbial genomes or chromosomes,each of which was prepared by a different sequen-cing group. The left side of the figure lists theoriginal entry; the right side of the figure shows acorrected version of the entry.

All of the entries in Figure 1 use different syntaxand semantics, and all violate the Genbank stan-dard in some way. In 1a, the product name is

Comparative and Functional GenomicsComp Funct Genom 2001; 2: 25–27.

Copyright # 2001 John Wiley & Sons, Ltd.

Fig

ure

1.

(1a–

3a)

Exce

rpts

from

thre

eG

enban

ken

trie

sth

atdo

not

confo

rmto

the

Gen

ban

kst

andar

d.(1

b–3b)

Corr

ecte

dve

rsio

ns

ofea

chen

try

that

do

confo

rmto

the

stan

dar

d

26 Conference Paper

Copyright # 2001 John Wiley & Sons, Ltd. Comp Funct Genom 2001; 2: 25–27.

prefixed with a variant of the gene name. Inexample 2a, the product qualifier simply repeatsthe gene name. The real product name, along withmuch other useful information, is buried in a textfield in a form that cannot be automatically parsedby a computer program. In the case of 3a, theunique ID is in the gene qualifier and the gene nameis appended to the product qualifier.

In addition, none of the entries has a labelqualifier containing the unique identifier associatedwith each coding region. Although the specificationdoes not require that the label qualifier be present,this unique identifier is useful for database linking.

A list of 11 non-conformant Genbank entries anda conversion of those entries to a form that doesmeet the standard is provided at http://www.ai.sri.com/pkarp/misc/gbkexample.html

Discussion

Although it is troubling that the sequencing projectsare not following the Genbank standard, it is evenmore troubling that the database staffs are notenforcing their own standards. An important role ofthe Genbank staff is ensuring that only high-qualitydata enter Genbank, which is the principal archiveof nucleotide-sequence information for the scientificcommunity. The Genbank staff should refuse toaccept entries that do not conform to the Genbankstandard. Although the staff might argue that theirresources are inadequate for policing every submis-sion to Genbank, we would argue that at least aminimal level of manual checking should beperformed for entries for complete genomes. Lite-rally 15 minutes of inspection would suffice to

identify many of the problems we have listed.Inspection of every coding sequence in a file isgenerally not necessary, because these files aretypically generated by programs that create thesame non-conformant fields in a systematic fashionfor every coding region.

Furthermore, some automated checks should beperformed on every incoming entry, such as veri-fying that the contents of the EC qualifier is a validEC number, verifying that the contents of the labelqualifier are unique across the entry, and verifyingthat a label qualifier is provided for every codingregion.

Some simple rules to remember when formulatingGenbank entries are:

$ Put each piece of information in the appropriatequalifier.

$ Supply as many qualifiers for each codingsequence as can reasonably be provided.

$ Do not attempt to be creative by addingadditional information into a given qualifier.For example, adding multiple synonyms for thegene name inside a given gene qualifier violatesthe specification and could produce erroneousresults in software that processes that qualifier.

See http://www.ai.sri.com/pkarp/misc/gbkexample.html for more examples of conformant Genbankentries.

Acknowledgements

This work was sponsored by Grant 1-R01-RR07861-01 from

the National Institutes of Health.

Conference Paper 27

Copyright # 2001 John Wiley & Sons, Ltd. Comp Funct Genom 2001; 2: 25–27.

Submit your manuscripts athttp://www.hindawi.com

Hindawi Publishing Corporationhttp://www.hindawi.com Volume 2014

Anatomy Research International

PeptidesInternational Journal of


Hindawi Publishing Corporation http://www.hindawi.com

International Journal of

Volume 2014

Zoology


Molecular Biology International

GenomicsInternational Journal of


The Scientific World JournalHindawi Publishing Corporation http://www.hindawi.com Volume 2014


BioinformaticsAdvances in

Marine BiologyJournal of



Signal TransductionJournal of


BioMed Research International

Evolutionary BiologyInternational Journal of



Biochemistry Research International

ArchaeaHindawi Publishing Corporationhttp://www.hindawi.com Volume 2014


Genetics Research International


Advances in

Virolog y

Hindawi Publishing Corporationhttp://www.hindawi.com

Nucleic AcidsJournal of

Volume 2014

Stem CellsInternational



Enzyme Research


International Journal of

Microbiology

many genbank entries for complete microbial genomes ... · the genbank staff is ensuring that only...

Documents