:: DESCRIPTION
HybridPSI is a new version of the tool in which the Smith-Waterman alignment algorithm core is replaced by the hybrid alignment algorithm.
::DEVELOPER
Ralf Bundschuh’s Statistical Physics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Jan 1;27(1):31-7. doi: 10.1093/bioinformatics/btq621. Epub 2010 Nov 24.
A performance enhanced PSI-BLAST based on hybrid alignment.
Li Y1, Chia N, Lauria M, Bundschuh R.
:: DESCRIPTION
SMI-BLAST (Supervised-Manner-based Iterative BLAST) is a novel supervised search framework based on PSI-BLAST for protein remote homology detection.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jin X, Liao Q, Wei H, Zhang J, Liu B.
SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection.
Bioinformatics. 2021 May 17;37(7):913-920. doi: 10.1093/bioinformatics/btaa772. PMID: 32898222.
:: DESCRIPTION
PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Margelevicius M., Venclovas C. (2005)
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability.
BMC Bioinformatics 6(1):185
:: DESCRIPTION
PeCoP stands for Persistently Conserved Positions. The PeCoP server offers a new way to examine positional conservation in protein sequences. The underlying rationale is that positions which are conserved in close and in distant sequence family members of the query sequence are more significant to the protein’s structure and function than those simply conserved in close family members. Positions which are conserved in close family members may be conserved due to evolutionary non-divergence, and therefore may not have a role in the protein’s structure or function. On the other hand, positions marked as conserved in distant family members may be marked as such due to errors in the multiple sequence alignment of remote sequences, which is tricky at best. The PeCoP server shows the conservation in varying degrees of family similarity to the query sequence, thus eliminating the false-positives that may be generated by alignments only to close and distant family members. It has been shown that this technique adds some 25% of information to the usual method of examining positional conservation in sequences, which is the “close-family” method.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Iddo Friedberg and Hanah Margalit
PeCoP: automatic determination of persistently conserved positions in protein families
Bioinformatics 2002 18: 1276-1277
:: DESCRIPTION
TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements. PSI-Blast is used with a collection of (retro-)transposon ORF homology profiles to identify statistically significant alignments. This method can be used to identify potential transposon ORFs within a protein set, or to identify regions of transposon homology within a larger genome sequence. This is particularly useful to identify degenerate transposon homologies within genome sequences that escape identification and masking by using RepeatMasker and an associated nucleotide library of repetitive elements. TransposonPSI has been routinely used to assist in the discovery of mobile elements across eukaryotes including protozoa, plants, fungi, and animals.
::DEVELOPER
Brian Haas @ Broad Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HangOut is a software for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
B.H. Kim, Q. Cong, N.V. Grishin (2010)
“HangOut: generating clean PSI-BLAST profiles for domains containing long insertions“.
Bioinformatics (2010) 26 (12): 1564-1565.
:: DESCRIPTION
SIB-BLAST (Simple Is Beautiful) is a novel algorithm developed to overcome the model corruption problem that occurs frequently in the later iterations of PSI-BLAST searches.The algorithm compares resultant hits from iteration two and the final iteration of a PSI-BLAST search, calculates the figure of merit for each “overlapped” hit and re-ranks the hits according to their figure of merit. The premise of the algorithm is based on the observation that the profile, namely, the position specific scoring matrix (PSSM), in the first two rounds of a PSI-BLAST search, is the least corrupted since it is comprised mostly of close homologs. These profiles are used to search for more distant homologs, which are used to generate subsequent PSSMs. As more distant homologs are incorporated into the PSSM, non-homologous sequences frequently get included also, thus leading to model corruption. Hence, “benchmarking” hits from later iteration against earlier round when the model is least corrupted should improve the accuracy of a PSI-BLAST search.
::DEVELOPER
Ralf Bundschuh‘s statistical physics group at the Department of Physics of The Ohio State University.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
M.M. Lee, M. Chan, and R. Bundschuh,
“Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches“,
Bioinformatics 24 (2008) 1339-1343.
