Sequence-alignment programs BLAST

The original bovine a-lactalbumin protein model was constructed before the availability of efficient sequence alignment programs and computational protein modeling applications. Instead of searching for similar sequences and structures using BLAST (because it did not exist), Browne et al. considered only four different solved protein structures as templates. To explore the... 

Sequence similarity search tools Alignments of the query sequence with databases produce sequence similarity. The BLAST series of programs has variants that will translate DNA databases, translate the input sequence, or both. FASTA provides a similar suite of programs. 

Database search programs like FASTA [18] or BLAST [19] have been optimised to detect evolutionary relationships between proteins, and are readily adequate for template recognition and (multiple) sequence alignment in cases where the sequence identity is over 25-30% [20], The general procedure is to assume next that the backbone of the model is identical to the one of the template structure and add the side chains onto it [21], although some difficulties may arise with insertions, deletions and local low similarity. 

Multiple sequence alignment of orthologues and paralogues (either BLAST multiple alignment or (preferably) other multiple alignment program)... 

QRNA is a program that utilizes BLAST-generated sequence alignments to identify patterns of sequence homology that likely represent conservation of RNA secondary structure (12). A putative sRNA identified by sRNAPredict2... 

---