Seedtop is part of the BLAST package from NCBI. seedtop answers two relatively simple questions: 1. Given a sequence and a database of patterns, which patterns occur in the sequence and where? 2. Given a pattern and a sequence database, which sequences contain the pattern and where?
Parent program: blast
BLAST is a software for comparing a query sequence with a library or database of sequences. BLAST identifies library hits that resemble the query above a certain threshold. Different types of BLASTs are designed according to the query and database types and search specificity (nucleotide blast implemented by blastn, megablast anddiscontiguousmegablast algorithms, protein blast by algorithms blastp, psi-blast, phi-blast, delta-blast, and three mixed types – blastx, tblastn, tblastx). Some specialized BLAST search types are also provided.