In the Using Bioinformatics: Genetic Research curriculum, students use BLAST to identify an unknown DNA sequence, perform multiple sequence alignments, and build phylogenetic trees (Table 2).
We used COMPASS and PHOG-BLAST to perform all-against-all comparisons between these 1254 PFAM alignments and to find BBHs.
We used BLAST [ 71] to perform homology searches against the SPtrEMBL protein database [ 14] (section 2.3) and against the NCBI's organism databases [ 61] (section 2.5) [see additional file 2], to study the phylogenetic distribution of the genes across model eukaryotic organisms.
The Basic Local Alignment Search Tool (BLAST) was used to perform annotation of R. philippinarum contigs.
Using to perform a BLAST search, we identified the genomic sequence of rat stathmin1 in a chromosome 5 contig.
Database analysis was performed using Blast and BLAT.
Homology searches were performed using Blast search in GenBank databases.
Predicted proteins were used as annotated, and an all-v-all BLAST comparison was performed using BLAST v2.2.26+ [ 13].
Sequence analysis was performed using Blast http://www.ncbi.nlm.nih.gov/blast/ against a non-redundant database.
Homology searches using specific gene sequences were performed using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi).nih.gov/Blast.cgi
