To perform an updated analysis of the distribution of Srx, we used BLAST to retrieve 335 Srx sequences from the nonredundant protein database.
Sequences of LRRCE motifs from the UniProt non-redundant set were used in similarity searches with BLAST to retrieve additional LRRCE-containing sequences (see Methods).
Therefore, the genes encoding such proteins can be easily retrieved using blast searches.
Excavate databases were searched using PSI-BLASTs independently to retrieve sequences with even the slightest resemblance to MVP.
BLAST outputs were parsed using Perl scripts to retrieve the best hit for each contig.
BLAST searches were used to retrieve non-annotated sequences from several mammalian genomes.
The basic local alignment search tool (BLAST) algorithm was used to retrieve for homologous sequences in GenBank.
Top blast hits for each transcript pairs were collected and filtered using bash scripting to retrieve 7547 pairs of transcripts showing identical hits to the same protein, which were subsequently utilized as ortholog pairs.
Gene ontology (GO) terms associated with the hits from BLASTx queries were then retrieved using the "Mapping" function in Blast2GO, which used BLAST accessions to link the queried sequences to functional information stored in the GO database (Gene Ontology Consortium 2008).
Accessions of BLAST hits were then used to retrieve associated sequence descriptions and GO terms.
