Tag: Pairwise

DeepAlign 1.35 – Pairwise Protein Structure Alignment

DeepAlign 1.35

:: 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 , Sheng Wang

:: 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.

PairwiseStatSig 20110801 – Pairwise Statistical Significance

PairwiseStatSig 20110801

:: DESCRIPTION

PairwiseStatSig estimates the pairwise statistical significance of a pairwise local alignment of two protein sequences independent of any database using censored Maximum Likelihood Fitting.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PairwiseStatSig

:: MORE INFORMATION

Citation

Agrawal, A., Brendel, V. & Huang, X. (2008)
Pairwise statistical significance versus database statistical significance for local alignment of protein sequences.
BMC Bioinformatics 2009, 10(Suppl 3):S1

LDheatmap 1.0-4 – Graphical Display of Pairwise Linkage Disequilibria between SNPs

LDheatmap 1.0-4

:: DESCRIPTION

LDheatmap is an R package implementing a graphical tool for exploring pairwise linkage disequilibria between Single Nucleotide Polymorphisms (SNPs).

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

:: DOWNLOAD

 LDheatmap

:: MORE INFORMATION

Citation

Ji-Hyung Shin, Sigal Blay, Brad McNeney, Jinko Graham
LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms
Journal of Statistical Software Vol. 16, Code Snippet 3, Sep 2006

Minimap2 v2.23 – Pairwise Alignment for Nucleotide Sequences

Minimap2 v2.23

:: DESCRIPTION

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Minimap2

:: MORE INFORMATION

Citation

Li H.
New strategies to improve minimap2 alignment accuracy.
Bioinformatics. 2021 Oct 8:btab705. doi: 10.1093/bioinformatics/btab705. Epub ahead of print. PMID: 34623391.

Li H.
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PMID: 29750242; PMCID: PMC6137996.

RL-CSA 20101023 – Regular-language Constrained Pairwise Global Sequence Alignment

RL-CSA 20101023

:: DESCRIPTION

RL-CSA is a tool for regular-language constrained pairwise global sequence alignment

::DEVELOPER

Michal Ziv-Ukelson’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

 RL-CSA

:: MORE INFORMATION

Citation

Kucherov, G., Pinhas, T., Ziv-Ukelson, M.:
Regular Language Constrained Sequence Alignment Revisited,
J Comput Biol. 2011 May;18(5):771-81.

deepTS – Exploring Transcriptional Switches from pairwise, temporal, and population RNA-Seq data

deepTS

:: DESCRIPTION

deepTS is a powerful and flexible web-based Galaxy platform for identifying, visualizing and analyzing transcriptional switch (TS) events from pairwise, temporal and population transcriptome data.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

deepTS

:: MORE INFORMATION

Citation

Qiu Z, Chen S, Qi Y, Liu C, Zhai J, Xie S, Ma C.
Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS.
Brief Bioinform. 2021 May 20;22(3):bbaa137. doi: 10.1093/bib/bbaa137. PMID: 32728687.

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

the Satija Lab

:: 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.

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.

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

Nakato lab

:: 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.

NgsRelate v2.0 – Estimating Pairwise Relatedness from NGS data

NgsRelate v2.0

:: 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