:: DESCRIPTION
Swat is a java commandline software based on dynamic programming to calculate optimal local alignments of DNA/RNA sequences and protein sequences.
::DEVELOPER
Medical Systems Biology, University of Ulm
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
Sprites is a sv caller that specializes in detecting deletion from low-coverage sequencing data. It works by identifying split reads from alignments based on soft-clipping information.
::DEVELOPER
Zhen Zhang (zhangz@csu.edu.cn)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sprites: detection of deletions from sequencing data by re-aligning split reads.
Zhang Z, Wang J, Luo J, Ding X, Zhong J, Wang J, Wu FX, Pan Y.
Bioinformatics. 2016 Feb 1. pii: btw053.
:: DESCRIPTION
PocketAlign is a web server of comparison of binding sites helps identify functional similarities and also identify drug cross-reactivities
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
No
:: MORE INFORMATION
Citation
J Chem Inf Model. 2011 Jul 25;51(7):1725-36. doi: 10.1021/ci200132z. Epub 2011 Jun 21.
PocketAlign a novel algorithm for aligning binding sites in protein structures.
Yeturu K, Chandra N.
:: DESCRIPTION
Opal is software for aligning multiple biological sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Multiple alignment by aligning alignments.
Wheeler TJ, Kececioglu JD.
Bioinformatics. 2007 Jul 1;23(13):i559-68.
:: DESCRIPTION
DAFS is a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment.
::DEVELOPER
Computational Biology Research Center (CBRC),
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y.
Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612.
:: DESCRIPTION
GR-Align (GRaphlet-based Aligner) is a fast heuristic procedure for aligning/comparing protein structures according to the Contact Map Opverlap maximization (CMO) paradigm. The algorithm is based on a Needleman-Wunch algorithm where the cost for matching two residues is their graphlet degree similarity.
GR-Align packages contains three software: CMap, DCount, and GR-Align:
CMap converts protein structures (.pdb) files into contact map graphs (leda graphs .gw)
DCount computes the graphlet degree signatures (.ndump files) from Contact Maps
GR-Align aligns protein structures (requieres both contact maps and signatures files)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 May 1;30(9):1259-65. doi: 10.1093/bioinformatics/btu020. Epub 2014 Jan 17.
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity.
Malod-Dognin N1, Pržulj N.
:: DESCRIPTION
Graemlin is a tool for aligning multiple global protein interaction networks; Graemlin also supports search for homology between a query module of proteins and a database of interaction networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Graemlin: general and robust alignment of multiple large interaction networks.
Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S.
Genome Res. 2006 Sep;16(9):1169-81
