:: DESCRIPTION
TwinCons is a software to detect noisy signals of deep ancestry of proteins or nucleic acids.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Penev PI, Alvarez-Carreño C, Smith E, Petrov AS, Williams LD.
TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
PLoS Comput Biol. 2021 Oct 29;17(10):e1009541. doi: 10.1371/journal.pcbi.1009541. PMID: 34714829; PMCID: PMC8580257.
:: DESCRIPTION
ProtDec-LTR is an method for protein remote homology detection by combining pseudo protein and supervised learning to rank
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Liu B, et al.
ProtDec-LTR3.0: protein remote homology detection by embedding sequence-based features into learning to rank,
IEEE ACCESS 2019; 7:102499-102507.
Chen J, Guo M, Li S, Liu B.
ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank.
Bioinformatics. 2017 Nov 1;33(21):3473-3476. doi: 10.1093/bioinformatics/btx429. PMID: 29077805.
Liu B, Chen J, Wang X.
Application of learning to rank to protein remote homology detection.
Bioinformatics. 2015 Nov 1;31(21):3492-8. doi: 10.1093/bioinformatics/btv413. Epub 2015 Jul 10. PMID: 26163693.
:: DESCRIPTION
miRNAminer is a web-based tool used for homologous miRNA gene search in several species. Given a search query, candidate homologs are identified using BLAST search and then tested for their known miRNA properties, such as secondary structure, energy, alignment and conservation, in order to assess their fidelity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2008 Jan 23;9:39. doi: 10.1186/1471-2105-9-39.
miRNAminer: a tool for homologous microRNA gene search.
Artzi S1, Kiezun A, Shomron N.
:: DESCRIPTION
HHalign-Kbest is useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yu J, Picord G, Tufféry P, Guerois R.
HHalign.KBest: exploring sub-optimal alignments for remote homology comparative modeling
Bioinformatics. 2015 Jul 30. pii: btv441.
:: DESCRIPTION
AlignNemo (Aligning Network Modules), is a novel algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that related in sequence and topology. The subnetworks have a general topology and need not to correspond to specific interaction patterns thus more closely fit the models of functional complexes proposed in the literature.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2012;7(6):e38107. Epub 2012 Jun 12.
AlignNemo: a local network alignment method to integrate homology and topology.
Ciriello G, Mina M, Guzzi PH, Cannataro M, Guerra C.
:: DESCRIPTION
NOmESS is a homolgy-driven assembly tool to create a NOn-redundant protEin Sequence Set for mass spectrometry.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Homology-driven assembly of NOn-redundant protEin Sequence Sets (NOmESS) for mass spectrometry.
Temu T, Mann M, Räschle M, Cox J.
Bioinformatics. 2016 Jan 6. pii: btv756.
:: DESCRIPTION
SANS is a program for searching protein sequence databases. It is as sensitive as BLAST when sequence identity is 50-100 %. SANS is faster than BLAST in batch mode. For example, a bacterial genome can be compared to Uniprot in one hour compared to 100 hours by BLAST.
SANSparallel takes a protein sequence as input and returns a set of similar sequences from Uniprot databases.
::DEVELOPER
Liisa Holm’s Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Sep 15;28(18):i438-i443. doi: 10.1093/bioinformatics/bts417.
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches.
Koskinen JP1, Holm L.
Nucleic Acids Res. 2015 Apr 8. pii: gkv317.
SANSparallel: interactive homology search against Uniprot.
Somervuo P, Holm L.
:: DESCRIPTION
DAPPLE is a homology-based method for predicting phosphorylation sites in an organism of interest. It uses BLAST searches of experimentally-determined phosphorylation sites in one organism (or several organisms) to predict phosphorylation sites in an organism of interest. It outputs a table containing information helpful for choosing phosphorylation sites that are of interest to you, such as the number of sequence differences between the query site and the hit site, the location of the query site and the hit site in their respective intact proteins, and whether the corresponding intact proteins are reciprocal BLAST hits (and thus predicted orthologues).
::DEVELOPER
Bioinformatics Research Group, University of Saskatchewan
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DAPPLE 2: a tool for the homology-based prediction of post-translational modification sites.
Trost B, Maleki F, Kusalik A, Napper S.
J Proteome Res. 2016 Jul 1.
Bioinformatics. 2013 Jul 1;29(13):1693-5. doi: 10.1093/bioinformatics/btt265. Epub 2013 May 8.
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.
Trost B, Arsenault R, Griebel P, Napper S, Kusalik A.
:: DESCRIPTION
SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).
::DEVELOPER
Protein Structure Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W252-8. doi: 10.1093/nar/gku340. Epub 2014 Apr 29.
:: DESCRIPTION
SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Aug 1;29(15):1858-64. doi: 10.1093/bioinformatics/btt313.
SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.
Porter MS, Beiko RG.
