LGSFAligner 01 – Align two RNA Secondary Structures Locally

LGSFAligner 01

:: DESCRIPTION

LGSFAligner (Local Gapped Subforest Aligner) is a tool to Align two RNA Secondary Structures Locally

::DEVELOPER

LGSFAligner team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 LGSFAligner

:: MORE INFORMATION

Citation:

J Comput Biol. 2006 Apr;13(3):702-18.
Local gapped subforest alignment and its application in finding RNA structural motifs.
Jansson J, Hieu NT, Sung WK.

BatMis 3.00 – Basic Alignment Tool for Mismatches

BatMis 3.00

:: DESCRIPTION

BatMis is a fast short read aligner allowing up to 10 mismatches

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  BatMis

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2122-8. doi: 10.1093/bioinformatics/bts339. Epub 2012 Jun 10.
BatMis: a fast algorithm for k-mismatch mapping.
Tennakoon C, Purbojati RW, Sung WK.

i-ADHoRe 3.0 – Detect Degenerated Genomic Homology

i-ADHoRe 3.0

:: DESCRIPTION

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  i-ADHoRe

:: MORE INFORMATION

Citation

i-ADHoRe 3.0–fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.
Nucleic Acids Res. 2012 Jan;40(2):e11. doi: 10.1093/nar/gkr955.

Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008)
i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles.
Bioinformatics 24, 127-8.

PathBLAST – Alignment of Protein Interaction Networks

PathBLAST

:: DESCRIPTION

PathBLAST searches the protein-protein interaction network of the target organism to extract all protein interaction pathways that align with a pathway query.

::DEVELOPER

the Ideker Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8.
PathBLAST: a tool for alignment of protein interaction networks.
Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T.

Belvu 20120403 – Multiple Alignments Viewer

Belvu 20120403

:: DESCRIPTION

Belvu is an X-windows viewer for multiple sequence alignments. One of the main advantages of Belvu is that it has an extensive set of modes to color the residues. There are several ways to color them by conservation and by residue type (user-configurable). Other useful features are fetching of the Swissprot (or PIR) entries by double clicking and easy tracking of the position in the alignment.

In addition, Belvu is a phylogenetic tool. It can be used to generate distance matrices between sequences under a selection of distance metrics. These can be saved and used subsequently in other applications. Belvu also implements certain distance-based tree reconstruction algorithms – including import of externally generated distance matrices – and bootstrap phylogenetic reconstruction. These functions are available both in the GUI (meaning Belvu may also be used as a tree viewer) or as command-line options, making the program a potential component in phylogenetic software pipelines.

::DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

Belvu

:: MORE INFORMATION

Citation:

Scoredist: A simple and robust protein sequence distance estimator
Erik LL Sonnhammer and Volker Hollich
BMC Bioinformatics 6:108 (2005)

SAMMate 2.7.4 / assemblySAM 1.1 – Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and Analysis

SAMMate 2.7.4 / assemblySAM 1.1

:: DESCRIPTION

SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

sammate

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • R package

:: DOWNLOAD

 SAMMate / assemblySAM

:: MORE INFORMATION

Citation:

Source Code Biol Med. 2011 Jan 13;6(1):2. doi: 10.1186/1751-0473-6-2.
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Xu G1, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.

Nguyen, T, Zhao, Z, Zhu, D.
SPATA: A seeding and patching algorithm for hybrid transcriptome assembly.

Nguyen, T, Deng, N, Zhu, D.
SASeq: A selective and adaptive shrinkage approach to detect and quantify active transcripts using RNA-Seq.

SeqTools 4.44.1 – A Suite of Tools for Visualising Sequence Alignments

SeqTools 4.44.1

:: DESCRIPTION

SeqTools is a suite of tools for visualising sequence alignments.

Blixem is an interactive browser of pairwise alignments that have been stacked up in a “master-slave” multiple alignment; it is not a ‘true’ multiple alignment but a ‘one-to-many’ alignment. It displays an overview section showing the positions of genes and alignments around the alignment window, and a detail section showing the actual alignment of protein or nucleotide sequences to the genomic DNA sequence.

Dotter is a graphical dot-matrix program for detailed comparison of two sequences. Every residue in one sequence is compared to every residue in the other, with one sequence plotted on the x-axis and the other on the y-axis. Noise is filtered out so that alignments appear as diagonal lines.

Belvu is a multiple sequence alignment viewer and phylogenetic tool. It has an extensive set of user-configurable modes to color residues by conservation or by residue type, and some basic alignment editing capabilities. It can generate distance matrices between sequences and construct distance-based trees, either graphically or as part of a phylogenetic software pipeline.

::DEVELOPER

the Annotools team at the Sanger Institute. seqtools@sanger.ac.uk

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • GTK+

:: DOWNLOAD

 SeqTools

:: MORE INFORMATION

Citation

A workbench for large-scale sequence homology analysis.
Sonnhammer EL and Durbin R
Computer applications in the biosciences : CABIOS1994;10;3;301-7

MORPH v0.1 beta – Probabilistic Alignment of Cis-regulatory Modules

MORPH v0.1 beta

:: DESCRIPTION

MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MORPH

:: MORE INFORMATION

Citation:

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.
Sinha S, He X.
PLoS Comput Biol. 2007 Nov;3(11):e216.

D2Z 0.1 – Alignment Free Comparison of Regulatory Sequences

D2Z 0.1

:: DESCRIPTION

D2Z is based on comparing the frequencies of all fixed-length words in the two sequences. An important, novel feature of the score is that it is comparable across sequence pairs drawn from arbitrary background distributions.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

D2Z Source Code

:: MORE INFORMATION

Citation:

A statistical method for alignment-free comparison of regulatory sequences
Miriam R. Kantorovitz,Gene E. Robinson, Saurabh Sinha.
Bioinformatics. 2007 Jul 1;23(13):i249-55.

Indelign 2.0.4 – Probabilistically Annotating Indels in Multiple Alignments

Indelign 2.0.4

:: DESCRIPTION

Indelign is a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Indelign

:: MORE INFORMATION

Citation:

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
Jaebum Kim and Saurabh Sinha
Bioinformatics. 2007 Feb 1;23(3):289-97.