Category: Alignment / BLAST

DiagAF 21.2.7 – Pre-Alignment Filter for Sequence Alignment

DiagAF 21.2.7

:: DESCRIPTION

DiagAF is a more accurate and efficient pre-alignment filter for sequence alignment. It can efficiently filter out candidates that contain errors greater than the edit distance threshold during read mapping.

::DEVELOPER

DiagAF team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DiagAF

:: MORE INFORMATION

Citation

Yu C, Zhao Y, Zhao C, Ma H, Wang G.
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Nov 17;PP. doi: 10.1109/TCBB.2021.3127879. Epub ahead of print. PMID: 34780330.

SNPsplit 0.5.0 – Allele-specific Alignment Sorting

SNPsplit 0.5.0

:: DESCRIPTION

SNPsplit is an allele-specific alignment sorter which is designed to read in alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Perl

:: DOWNLOAD

SNPsplit

:: MORE INFORMATION

Citation

Krueger F, Andrews SR.
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes.
F1000Res. 2016 Jun 23;5:1479. doi: 10.12688/f1000research.9037.2. PMID: 27429743; PMCID: PMC4934512.

FACS 2.1 – Align Sequences to a Reference Sequence

FACS 2.1

:: DESCRIPTION

A novel algorithm, FACS (Fast and Accurate Classification of Sequences), is introduced that can accurately and rapidly align sequences to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS is at least three times faster and more accurate than BLAT and SSAHA2 in classifying sequences when using references larger than 50Mbp.

::DEVELOPER

the Science for Life Laboratory, Uppsala University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Perl

:: DOWNLOAD

 FACS

:: MORE INFORMATION

Citation

Stranneheim H, Käller M, Allander T, Andersson B, Arvestad L, Lundeberg J.
Classification of DNA sequences using Bloom filters.
Bioinformatics, 2010 July 1; 26(13):1595-1600. Published online 2010 May 13. doi:10.1093/bioinformatics/btq230

FRUUT 2.46 – Fast RNA Unrooted Unordered Tree Alignment

FRUUT 2.46

:: DESCRIPTION

FRUUT computes an RNA structure alignment of two given RNA molecules. We generalize previous algorithms that either solved the problem in an asymmetric manner, or were restricted to the rooted and/or ordered cases. Focusing here on the most general unrooted unordered case, we show that our algorithm has an O(nTnS min(dT, dS)) time complexity, where nT and nS are the number of nodes and dT and dS are the maximum node degrees in the input trees T and S, respectively. This maintains (and slightly improves) the time complexity of previous, less general algorithms for the problem.

::DEVELOPER

Michal Ziv-Ukelson’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

 FRUUT

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2013 Apr 16;8(1):13. doi: 10.1186/1748-7188-8-13.
Unrooted unordered homeomorphic subtree alignment of RNA trees.
Milo N1, Zakov S, Katzenelson E, Bachmat E, Dinitz Y, Ziv-Ukelson M.

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.

Seqotron v1.0.1 – Alignment Editor for Mac OS X

Seqotron v1.0.1

:: DESCRIPTION

Seqotron is a user-friendly sequence editor. It is written in Objective-C/Cocoa and runs on Mac OS X.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

Seqotron

:: MORE INFORMATION

CitationFourment M, Holmes EC.
Seqotron: a user-friendly sequence editor for Mac OS X.
BMC Res Notes. 2016 Feb 17;9:106. doi: 10.1186/s13104-016-1927-4. PMID: 26887850; PMCID: PMC4756450.

 

CAT / Xat 0.8.6 – Cross-species Alignment Tool

CAT / Xat 0.8.6

:: DESCRIPTION

 CAT (Xat) is designed to be a cross-species (both intra-species and inter-species), nucleotide level, cDNA-to-genome alignment software. It uses improved heuristics to effectively balance specificity, sensitivity and speed, and is optimized for genome-wide mapping.

::DEVELOPER

CAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 CAT / Xat

:: MORE INFORMATION

Citation

A cross-species alignment tool (CAT).
Li H, Guan L, Liu T, Guo Y, Zheng WM, Wong GK, Wang J.
BMC Bioinformatics. 2007 Sep 19;8:349.

SWeBLAST – Look for Recombinations in non-aligned Sequences using BLAST

SWeBLAST

:: DESCRIPTION

SWeBLAST (Sliding Window Web-based BLAST) is a perl program that looks for recombinations in non-aligned sequences using BLAST.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 SWeBLAST

:: MORE INFORMATION

Citation

Fourment M, Gibbs AJ, Gibbs MJ.
SWeBLAST: a Sliding Window Web-based BLAST tool for recombinant analysis.
J Virol Methods. 2008, 152, 98-101