Format

Send to:

Choose Destination
See comment in PubMed Commons below
In Silico Biol. 2006;6(5):363-72.

Efficient secondary database driven annotation using model organism sequences.

Author information

  • 1Departamento de Bioquimica e Imunologia, ICB-UFMG, 31270-010, Brazil.

Abstract

The use of sequences from specific organisms for annotation requires that it does not represent great loss of information and that the sequences available suffice for annotation. In order to investigate whether or not sequences from model organisms may suffice for annotation of sequences from the trematode Schistosoma mansoni, we performed local BLAST searches of S. mansoni sequences against other organisms sequences present in the NCBI database nr. Results have been inserted into a relational database and hits to sequences from three model organisms, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens have been computed and compared to hits to sequences from other organisms present in nr; score values of each alignment have also been registered. Our observations have shown that a large fraction of orthologous proteins exists in the set of sequences from the three model organisms selected, and therefore a similar fraction of transcripts can be annotated when using either nr or model organism datasets. Moreover, hits to model organisms' sequences are largely as informative as nr. Results suggest that model organisms provide a reliable set of sequences to use as a reference database for S. mansoni sequence annotation, showing the clear possibility of using a restricted dataset of expected better quality for functional annotation and therefore supporting secondary database driven annotation approaches.

PMID:
17274765
[PubMed - indexed for MEDLINE]

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases

PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for IOS Press
    Loading ...
    Write to the Help Desk