:: DESCRIPTION
Mattbench is a protein structural alignment benchmark that may be used to test and refine protein sequence aligners.
::DEVELOPER
Bioinformatics and Computational Biology Research Group, Tufts University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
IEEE/ACM Trans Comput Biol Bioinform. 2012 Jan-Feb;9(1):286-93. doi: 10.1109/TCBB.2011.70.
Touring protein space with Matt.
Daniels NM, Kumar A, Cowen LJ, Menke M.
:: DESCRIPTION
Formatt is a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments.
::DEVELOPER
Bioinformatics and Computational Biology Research Group, Tufts University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2012 Oct 6;13:259. doi: 10.1186/1471-2105-13-259.
Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.
Daniels NM, Nadimpalli S, Cowen LJ.
:: DESCRIPTION
Seal is a suite of distributed applications for aligning short DNA reads, and manipulating and analyzing short read alignments. Seal applications generally run on the Hadoop framework and are made to scale well in the amount of computing nodes available and the amount of the data to process. This fact makes Seal particularly well suited for processing large data sets. Seal is part of the Biodoop suite of tools.
::DEVELOPER
Luca Pireddu, Simone Leo and Gianluigi Zanetti
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Aug 1;27(15):2159-60. doi: 10.1093/bioinformatics/btr325.
SEAL: a distributed short read mapping and duplicate removal tool.
Pireddu L, Leo S, Zanetti G.
:: DESCRIPTION
MitoScape is a novel, big-data, software for extracting mitochondrial DNA sequences from NGS.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Singh LN, Ennis B, Loneragan B, Tsao NL, Lopez Sanchez MIG, Li J, Acheampong P, Tran O, Trounce IA, Zhu Y, Potluri P; Regeneron Genetics Center, Emanuel BS, Rader DJ, Arany Z, Damrauer SM, Resnick AC, Anderson SA, Wallace DC.
MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data.
PLoS Comput Biol. 2021 Nov 11;17(11):e1009594. doi: 10.1371/journal.pcbi.1009594. Epub ahead of print. PMID: 34762648.
:: DESCRIPTION
The SHERA software turns error-prone short reads into Sanger-quality composite reads by aligning the overlapping ends of each matepair. Given a library of appropriately-sized inserts, paired-end reads of each insert overlap in the middle, and can be aligned to produce a longer, more accurate composite read, extending the scope of applications for high throughput shortread sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, et al. (2010)
Unlocking Short Read Sequencing for Metagenomics.
PLoS ONE 5(7): e11840. doi:10.1371/journal.pone.0011840
:: DESCRIPTION
PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii237-42.
RNA secondary structural alignment with conditional random fields.
Sato K, Sakakibara Y.
:: DESCRIPTION
InterEvol PyMOL is a pymol plugin to perform structure-oriented exploration of the sequence alignments.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Jan;40(Database issue):D847-56. doi: 10.1093/nar/gkr845. Epub 2011 Nov 3.
InterEvol database: exploring the structure and evolution of protein complex interfaces.
Faure G1, Andreani J, Guerois R.
:: DESCRIPTION
MISTRAL is a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules.
::DEVELOPER
The Institut de Physique Théorique (IPhT)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Oct 15;25(20):2663-9. doi: 10.1093/bioinformatics/btp506. Epub 2009 Aug 19.
MISTRAL: a tool for energy-based multiple structural alignment of proteins.
Micheletti C1, Orland H.
:: DESCRIPTION
TREMOLO-HCA (Traveling into REmote hoMOLOgy with HCA) is a tool for the analysis of distant relationships between protein sequences. It allows an easier interpretation of the PSI-BLAST results by adding information on the domain architecture (deduced from the CDD database) of proteins with which the query sequence is aligned, as well on the conservation of hydrophobic amino acids that may be critical for the fold. HCA plots of the aligned sequences can also be displayed, allowing their comparison at the 2D level.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jul 15;29(14):1726-33. doi: 10.1093/bioinformatics/btt271. Epub 2013 May 14.
Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information.
Faure G1, Callebaut I.