CottonGen offers BLAST with genome, transcriptome, peptide and marker sequence databases from Gossypium species.  This can be done using nucleotide sequences (Fig. 29A) or peptide sequences (Fig. 29B).  BLAST functionality is similar to that on NCBI, and information on advanced settings can be found in the NCBI BLAST Help manual.

Figure 29.  BLAST menu on CottonGen.

The new Tripal BLAST module displays results in an interactive interface where target hit alignment and quality can be viewed (Fig. 30A).  Features that are in the CottonGen database will have links to their CottonGen entries where further information can be found (Fig. 30B), and alignments to genome scaffolds that are in CottonGen JBrowse will have links to JBrowse.

Figure 30.  BLAST results in CottonGen.