How does HHblits work?
HHblits, a part of the HH-suite since 2001, builds high-quality multiple sequence alignments (MSAs) starting from a single query sequence or a MSA. As in PSI-BLAST, it works iteratively, repeatedly constructing new query profiles by adding the results found in the previous round.
How does HHpred work?
HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. A detailed help facility is available.
What is a Psi-Blast?
Position-Specific Iterative (PSI)-BLAST is a protein sequence profile search method that builds off the alignments generated by a run of the BLASTp program. The first iteration of a PSI-BLAST search is identical to a run of BLASTp program (1).
What is UniRef90?
UniRef90 is built by clustering UniRef100 sequences such that each cluster is composed of sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence in the cluster (the seed sequence).
Why multiple sequence alignment is important?
Abstract. Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families.
What is UniParc?
The UniProt Archive (UniParc) is a comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world. Proteins may exist in different source databases and in multiple copies in the same database.
What is Psi and Phi-BLAST?
PSI-BLAST considers position-specific information when searching for significant hits. PHI-BLAST uses a pattern, or profile, to seed an alignment, which is then extended by the normal BLASTP algorithm.
What is Phi-BLAST used for?
PHI-BLAST (Pattern-Hit Initiated BLAST) is a search program that combines matching of regular expressions with local alignments surrounding the match.
What is Delta-BLAST used for?
DELTA-BLAST searches a protein sequence database using a PSSM constructed from conserved domains matching a query. It first searches the NCBI CDD database to construct the PSSM.
What are the differences between PSI BLAST and Delta-BLAST?
DELTA-BLAST is similar to PSI-BLAST but in the first search it uses a Conserved Domain Database. With the results creates a PSSM and uses that to search in the protein database.