Category: Sequence - Pairwise Similarity

Programs:

• align - Pairwise global sequence alignment
• bestscor - Calculate the score of a 100% identical match
• blastcl3 - run BLAST remotely at NCBI
• d3hom - Dot-matrix DNA similarity, k=3
• d4hom - Dot-matrix DNA similarity, k=4
• fasta - Sequence database similarity
• ggsearch - global alignment of two DNA or protein sequences
• glsearch - global alignment of DNA or protein query sequence with local alignments of database sequences
• lalign - Rigorous local pairwise alignment
• p1hom - Dot-matrix protein similarity, k=1
• p2hom - Dot-matrix protein similarity, k=2
• relate - Statistical significance of database similarity
• tfasta - Database similarity with translated DNA database
• tfastx - compare a protein to a DNA database, calculating similarities with frameshifts
• tfasty - compare a protein to a DNA database, calculating similarities with frameshifts