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PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families. The unclassified proteins are grouped according to similarity.
The open-source software MMseqs is an alternative to BLAST/PSI-BLAST, which improves on current search tools over the full range of speed-sensitivity trade-off, achieving sensitivities better than PSI-BLAST at more than 400 times its speed. [27]
PSI-blast based secondary structure PREDiction (PSIPRED) is a method used to investigate protein structure. It uses artificial neural network machine learning methods in its algorithm. [ 2 ] [ 3 ] [ 4 ] It is a server-side program, featuring a website serving as a front-end interface, which can predict a protein's secondary structure ( beta ...
CS-BLAST greatly improves alignment quality over the entire range of sequence identities and especially for difficult alignments in comparison to regular BLAST and PSI-BLAST. PSI-BLAST (Position-Specific Iterated BLAST) runs at about the same speed per iteration as regular BLAST, but is able to detect weaker sequence similarities that are still ...
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Psi is an ab initio computational chemistry package originally written by the research group of Henry F. Schaefer, III (University of Georgia). Utilizing Psi, one can perform a calculation on a molecular system with various kinds of methods such as Hartree-Fock , Post-Hartree–Fock electron correlation methods, and density functional theory .
A BLAST variant called MegaBLAST indexes 4 databases to speed up alignments. [ 9 ] BLAT can extend on multiple perfect and near-perfect matches (default is 2 perfect matches of length 11 for nucleotide searches and 3 perfect matches of length 4 for protein searches), while BLAST extends only when one or two matches occur close together.
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