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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]
Linking and profiling sequence alignment data from NCBI-BLAST results with major sequence analysis servers/services: Nucleotide, peptide: 2010 SAM Local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST: Both: Karplus K, Krogh A [15] 1999 SSEARCH Smith-Waterman search, slower but more sensitive than FASTA: Both ...
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.
Version number 5 Table version number. Incremented when data is changed and wrapped around on overflow for values greater than 32. Current/next indicator 1 Indicates if data is currently in effect or will be made effective in the near future. If the bit is 1, the data is to be used now. If 0, the decoder may begin to prepare for the data to change.
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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Although EXALIN performed full dynamic programming by default, it could optionally utilize the output from WU-BLAST to seed the dynamic programming and speed up the process by about 100-fold with little loss of sensitivity or accuracy. In 2008, Gish founded Advanced Biocomputing, LLC, where he continues to improve and support the AB-BLAST package.