brief description of:

Buchnera^bbp a·n·n·o·t·a·t·i·o·n methods

 

• Gene annotation

• coding genes and pseudogenes: The identification of open reading frames started with the use of orfind [1]. These predictions were refined by both using the programs genmark [2] and glimmer [3] and by hand-curation.
Pseudogenes were identified from this results and by looking for similarities to real coding sequences using blast [4].
• tRNA identification: it was carried using the program tRNAscan-SE [5].
• rRNA and other RNAs: they were identified doing blast-searches with the intergenic regions versus prokaryotic DNA from GenBank and their limits were hand-curated.

• Functional annotations

• Functional classification: the guidelines proposed by Shigenobu et al. (2000) [6] where applied for better comparison, which are based on the functional classification of the Riley's schema [7].
• Function annotation (functional descriptions, E.C. numbers, keywords):  For deriving a functional description for each protein, the FUNCut program [8] was used. This program do (recursive or simple) BLAST searches to collect similar sequences, then aligns all versus all to obtain a measure of the distance between all possible pairs. This way, a representation of the sequence space is obtained, and a clustering algorithm [9] tries to detect  differentiated groups of sequences in that space, that ideally will belong to a common subfamily, in which function is expected to be conserved. The 'subfamily' of the problem sequence is retrieved and its sequences annotations inspected to distill: 1) a representative function description; 2) enzymatic activities (EC numbers); and 3) keywords.

This automatic annotations were also refined by hand. The hand-curated and automatic annotations are provided by the server.
• COGs [10] assignment:  For the assignment of COGs we identified the orthology relationships between the two buchneras (the APS one is annotated at COGs), and transfer the annotation from Buchenera ^APS to buchnera ^BBP. The coverage of the alignments was inspected to take into account when a BBP gene was fragmented in two genes in APS. For the cases in which there was no ortholog in APS, the program COGnitor [11] was used for the assignment.
 
 
 
• Information storage and WEB access

 
The information derived from these methods and some other such as BLAST results were stored in a relational database (ORFandDB [12]). A web interface was build to access this information [13].
 

 
• References

 
·1:  NCBI: Tatusov T, Tatusov R.
http://www.ncbi.nlm.nih.gov/gorf/gorf.html

·2:  Lukashin AV, Borodovsky M.
GeneMark.hmm: new solutions for gene finding.
Nucleic Acids Res. 1998 Feb 15;26(4):1107-15.

·3:  Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL.
A probabilistic method for identifying start codons in bacterial genomes.
Bioinformatics. 2001 Dec;17(12):1123-30.

·4:  Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.

·5:  Lowe TM, Eddy SR.
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Nucleic Acids Res. 1997 Mar 1;25(5):955-64.

·6:  Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H.
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS.
Nature. 2000 Sep 7;407(6800):81-6.

·7:  Riley M.
Functions of the gene products of Escherichia coli.
Microbiol Rev. 1993 Dec;57(4):862-952.

·8:  Unpublished.

·9:  Abascal F, Valencia A.
Clustering of proximal sequence space for the identification of protein families.
Bioinformatics. 2002. In press.

·10:  Tatusov RL, Koonin EV, Lipman DJ.
A genomic perspective on protein families.
Science. 1997 Oct 24;278(5338):631-7.

·11:  NCBI.
http://www.ncbi.nlm.nih.gov/COG/xognitor.html

·12: Unpublished.

·13: PDG.
http://www.pdg.cnb.uam.es/fabascal/Buch_ORFand_www
 
 
 


 
 

 
 
 
 

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