GapsMis 0.0.0 / GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.9 – Pairwise Short-read Alignment

GapsMis 0.0.0 / GapMis 0.0.7 / GapMis-OMP 0.0.2 / libgapmis 0.0.9

:: DESCRIPTION

GapsMis is a tool for pairwise sequence alignment with a bounded number of gaps.

GapMis is a tool for pairwise sequence alignment with a single gap.

GapMis-OMP is the OpenMP-based version of GapMis.

libgapmis is an ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • EMBOSS
  • Python
  • C Compiler

:: DOWNLOAD

 GapsMisGapMis , GapMis-OMP , libgapmis 

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.
libgapmis: extending short-read alignments.
Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.

GapMis: a tool for pairwise sequence alignment with a single gap.
Flouri T, Frousios K, Iliopoulos CS, Park K, Pissis SP, Tischler G.
Recent Pat DNA Gene Seq. 2013 Aug;7(2):84-95.

Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, and German Tischler.
Approximate string-matching with a single gap for sequence alignment.
In Proceedings of the Second ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2011), pp. 490-492, 2011. ACM Digital Library

NW 3.12 – Pairwise Needleman and Wunsch Sequence Alignment program

NW 3.12

:: DESCRIPTION

NW is an implementation of the Needleman and Wunsch dynamic programming sequence alignment algorithm. It reads PIR format sequence files and reports sequence similarity calculated in a number of different ways. Optionally it can generate a PIR format alignment file.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NW

:: MORE INFORMATION

CONSAN 1.2 – Pairwise Structural RNA Alignment

CONSAN 1.2

:: DESCRIPTION

CONSAN is a software of pairwise RNA structural alignment, both unconstrained and constrained on alignment pins.

::DEVELOPER

Robin Dowell, Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CONSAN

:: MORE INFORMATION

Citation

Dowell, RD and Eddy, SR.
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.
BMC Bioinformatics 2006, 7:400 .

NgsRelate – Estimating Pairwise Relatedness from NGS data

NgsRelate

:: DESCRIPTION

NgsRelate can be used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.

::DEVELOPER

NgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 NgsRelate

:: MORE INFORMATION

Citation

NgsRelate: a software tool for inferring pairwise relatedness from Next Generation Sequencing data.
Korneliussen TS, Moltke I.
Bioinformatics. 2015 Aug 30. pii: btv509

UniAlign – Protein Pairwise Structure Alignment with Evolution and Sequence Information

UniAlign

:: DESCRIPTION

UniAlign is a new protein pairwise structure alignment algorithm that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles, and residue conservation.

::DEVELOPER

Sacan Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

 

:: MORE INFORMATION

Citation

UniAlign: Protein Structure Alignment Meets Evolution.
Zhao C, Sacan A.
Bioinformatics. 2015 Jun 9. pii: btv354.

BEAGLE – Pairwise RNA Structural Alignment

BEAGLE

:: DESCRIPTION

BEAGLE (BEar Alignment Global and Local) is a new alignment tool exploiting a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform global and local alignments.

::DEVELOPER

BEAGLE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Web-Beagle: a web server for the alignment of RNA secondary structures.
Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M.
Nucleic Acids Res. 2015 May 14. pii: gkv489.

GRAPeFoot 20101217 – Pairwise (Genome) Re-aligner and Phylogenetic Footprinter

GRAPeFoot 20101217

:: DESCRIPTION

GRAPeFoot simultaneously aligns two full genomes and annotates a set of conserved regions exhibiting reduced rates of insertion, deletion and substitution mutations.

::DEVELOPER

Dr. Rahul Satija

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GRAPeFoot

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2116-20. doi: 10.1093/bioinformatics/btq360. Epub 2010 Jul 7.
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.
Satija R1, Hein J, Lunter GA.

DeepAlign 1.13 – Pairwise Protein Structure Alignment

DeepAlign 1.13

:: DESCRIPTION

Different from many other tools, DeepAlign aligns two protein structures using evolutionary information and beta strand orientation in addition to geometric similarity. Therefore, DeepAlign favors the alignment of evolutionarily-related residues and also aligns beta sheets more correctly than the others. The DeepAlign alignments are also much more consistent with manual alignments than the others.

::DEVELOPER

Xu group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DeepAlign

:: MORE INFORMATION

Citation:

Sci Rep. 2013;3:1448. doi: 10.1038/srep01448.
Protein structure alignment beyond spatial proximity.
Wang S, Ma J, Peng J, Xu J.

CGALN 1.2.3 – Pairwise Genomic Sequence Alignment Program

CGALN 1.2.3

:: DESCRIPTION

Cgaln (Coarse grained alignment) is a program designed to align a pair of whole genomic sequences of not only bacteria but also entire chromosomes of vertebrates on a nominal desktop computer. Cgaln performs an alignment job in two steps, at the block level and then at the nucleotide level. The former “coarse-grained” alignment can explore genomic rearrangements and reduce the regions to be analyzed in the next step. The latter is devoted to detailed alignment within the limited regions found in the first stage. The output of Cgaln is ‘glocal’ in the sense that rearrangements are taken into consideration while each alignable region is extended as long as possible. Thus, Cgaln is not only fast and memory-efficient, but also can filter noisy outputs without missing the most important homologous segment pairs.

::DEVELOPER

Ryuichiro NAKATO, Osamu Gotoh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 CGALN

:: MORE INFORMATION

Citation

Nakato, R., and Gotoh, O. (2010)
Cgaln: fast and space-efficient whole-genome alignment,
BMC Bioinformatics 11, 224.

Comintern 1.0 – Computing Pairwise Common Intervals

Comintern 1.0

:: DESCRIPTION

Comintern contains python scripts to compute common intervals between two linear genomes.  It can also be applied to find common intervals between any two sequences, wether or not they represent genomes, provided they are encoded in a genome format.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Comintern

:: MORE INFORMATION

Citation

Thomas Schmidt, Jens Stoye
Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences
Lecture Notes in Computer Science Volume 3109, 2004, pp 347-358