InDelFixer 1.1 – An Insertion and Deletion Fixing Aligner for 454, Illumina and PacBio

InDelFixer 1.1

:: DESCRIPTION

InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 InDelFixer

:: MORE INFORMATION

ABMapper 2.0.4 – A suffix-array based Spliced Alignment tool

ABMapper 2.0.4

:: DESCRIPTION

ABMapper is a portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.

::DEVELOPER

ABMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Perl

:: DOWNLOAD

  ABMapper

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):421-2. doi: 10.1093/bioinformatics/btq656. Epub 2010 Dec 17.
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.
Lou SK, Ni B, Lo LY, Tsui SK, Chan TF, Leung KS.

SNAP 20080926 / FlexSnap 20091128 – Non-sequential Pair-wise Structural Alignment

SNAP 20080926 / FlexSnap 20091128

:: DESCRIPTION

SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA

FlexSnap allows the ability to find both flexible and non-sequential allignments.

::DEVELOPER

Mohammed J. Zaki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SNAP , FlexSnap

:: MORE INFORMATION

Citation

Saeed Salem, Mohammed J. Zaki and Chris Bystroff,
Iterative Non-Sequential Protein Structural Alignment.
Journal of Bioinformatics and Computational Biology, 7(3):571-596. Jun 2009

Algorithms Mol Biol. 2010 Jan 4;5:12. doi: 10.1186/1748-7188-5-12.
FlexSnap: flexible non-sequential protein structure alignment.
Salem S1, Zaki MJ, Bystroff C.

RNAmountAlign – RNA Sequence/Structure Alignment

RNAmountAlign

:: DESCRIPTION

RNAmountAlign is a novel algorithm for RNA sequence/structure pairwise alignment, that runs in O(n3) time and O(n2) space; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics as well as parameter fitting.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAmountAlign

:: MORE INFORMATION

Citation:

PLoS One, 15 (1), e0227177 2020 Jan 24 eCollection 2020
RNAmountAlign: Efficient Software for Local, Global, Semiglobal Pairwise and Multiple RNA Sequence/Structure Alignment
Amir H Bayegan , Peter Clote

Gibbs Motif Sampler 3.2 – Identify Motifs, Conserved Regions, in DNA or Protein Sequences

Gibbs Motif Sampler 3.2

:: DESCRIPTION

The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.

::DEVELOPER

Wadsworth Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows with Cygwin/MacOsX

:: DOWNLOAD

 Gibbs Motif Sampler

:: MORE INFORMATION

Citation

Neuwald AF, Liu JS, and Lawrence CE. (1995)
Gibbs motif sampling: detection of bacterial outer membrane protein repeats.
Protein Sci 4(8):1618-1632. PubMed: 8520488.

UnderII – Regulatory Sequences Comparison

UnderII

:: DESCRIPTION

UnderII is a software of alignment-free comparison of regulatory sequences (cis-regulatory modules).

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderII

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jul-Aug;11(4):628-37. doi: 10.1109/TCBB.2014.2306830.
Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison.
Comin M, Verzotto D.

Matt 1.0 – Multiple Protein Structure Alignment program

Matt 1.0

:: DESCRIPTION

Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows

:: DOWNLOAD

  Matt

:: MORE INFORMATION

Citation:

M. Menke, B. Berger, L. Cowen,
Matt: Local Flexibility Aids Protein Multiple Structure Alignment“,
PLOS Computational Biology, Vol. 4, No 1., 2008.

GLASS – Aligns large Orthologous Genomic Regions

GLASS

:: DESCRIPTION

GLASS (GLobal Alignment SyStem) is a tool for aligning pairs of homologous sequences. It is designed for aligning long, divergent sequences, that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 GLASS

:: MORE INFORMATION

Citation:

S. Batzoglou, L. Pachter, J.P. Mesirov, B. Berger, and E.S. Lander.
Human and mouse Gene Structure: Comparative Analysis and Application to Exon Prediction.
Genome Research, July 1, 2000.

CAST 1.2.2 – Compression-accelerated BLAST and BLAT

CAST 1.2.2

:: DESCRIPTION

CAST is a set of tools that compress data in a way that allows direct computation on the compressed data. Compression-accelerated BLAST (CaBLAST) and Compression-accelerated BLAT (CaBLAT) are two prototype implementations of alignment and sequence search algorithms that apply “compressive genomics” : i.e., they exploit redundancy in genomic data sets by compressing data in a way that allows direct computation on the compressed data.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ Compiler
  • NCBI C++ Toolkit
  • BLAST+
  • BLAT

:: DOWNLOAD

  CAST

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2012 Jul 10;30(7):627-30. doi: 10.1038/nbt.2241.
Compressive genomics.
Loh PR, Baym M, Berger B.

CaBLASTP 1.0.3 – Performs BLAST on Compressed Proteomic data

CaBLASTP 1.0.3

:: DESCRIPTION

CaBLASTP is a suite of homology search tools, powered by compressively-accelerated protein BLAST, which are significantly faster than and comparably accurate to all known state-of- the-art tools including HHblits, DELTA-BLAST, and PSI-BLAST. Further, our tools are implemented in a manner that allows direct substitution into existing analysis pipelines.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • BLAST+

:: DOWNLOAD

 CaBLASTP

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 1;29(13):i283-90. doi: 10.1093/bioinformatics/btt214.
Compressive genomics for protein databases.
Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B.