PHMMTS 20070918 – Aligns Sequence to Sequence of Known Secondary Structure

PHMMTS 20070918

:: DESCRIPTION

PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure.

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows with MinGW32

:: DOWNLOAD

 PHMMTS

:: MORE INFORMATION

Citation:

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii237-42.
RNA secondary structural alignment with conditional random fields.
Sato K, Sakakibara Y.

AlphaMALIG 1.1 – Aligns Sequences in a given Alphabet

AlphaMALIG 1.1

:: DESCRIPTION

AlphaMALIG  (ALPHAbet Multiple ALIGnment) is a tool which allows you to align many but no more than 200 sequences. These sequences will be formed by characters of a finite alphabet.

::DEVELOPER

 the Algorithmics and Genetics Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C compiler

:: DOWNLOAD

  AlphaMALIG

:: MORE INFORMATION

deepBlockAlign 1.3.1 – Align RNA-seq Profiles of Read Block Patterns.

deepBlockAlign 1.3.1

:: DESCRIPTION

deepBlockAlign is a tool for aligning RNA-seq profiles of read block patterns.The analysis starts from closely spaced blocks of mapped reads, which we call block groups.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 deepBlockAlign

:: MORE INFORMATION

Citation:

Langenberger, D., Pundhir, S., Ekstrøm, C.T., Stadler, P.F., Hoffmann, S., and Gorodkin, J. (2011).
deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns.
Bioinformatics. 2012 Jan 1;28(1):17-24. doi: 10.1093/bioinformatics/btr598

ArkMAP 2.78 – Draw and Align Genetic Maps

ArkMAP 2.78

:: DESCRIPTION

ArkMAP is a desktop application that allows users to draw and align genetic maps.

::DEVELOPER

Roslin Bioinformatics

:: SCREENSHOTS

ArkMAP

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Java

:: DOWNLOAD

 ArkMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 13;14:246. doi: 10.1186/1471-2105-14-246.
ArkMAP: integrating genomic maps across species and data sources.
Paterson T, Law A.

DualAligner v1.0 – Dual Alignment-based Strategy to Align Protein Interaction Networks

DualAligner v1.0

:: DESCRIPTION

DualAligner performs dual network alignment, in which both region-to-region alignment, where whole subgraph of one network is aligned to subgraph of another, and protein-to-protein alignment, where individual proteins in networks are aligned to one another, are performed to achieve higher accuracy network alignments.

::DEVELOPER

Computational Systems Biology Research Group(COSBY)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

DualAligner

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 28. pii: btu358. [Epub ahead of print]
DualAligner: A Dual Alignment-based Strategy to Align Protein Interaction Networks.
Seah BS1, Bhowmick SS2, Dewey CF Jr3.

LASTZ 1.04.03 – Program for Aligning DNA Sequences

LASTZ 1.04.03

:: DESCRIPTION

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

::DEVELOPER

Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  LASTZ

:: MORE INFORMATION

Citation:

Harris, R.S. (2007)
Improved pairwise alignment of genomic DNA.
Ph.D. Thesis, The Pennsylvania State University.

SMALT 0.7.6 – Align DNA Sequencing Reads with Genomic Reference Sequences

SMALT 0.7.6

:: DESCRIPTION

SMALT efficiently aligns DNA sequencing reads with genomic reference sequences.

::DEVELOPER

Hannes Ponstingl.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMALT

:: MORE INFORMATION

AREM 1.0.1 – Aligning Short Reads from ChIP-sequencing by Expectation Maximization

AREM 1.0.1

:: DESCRIPTION

AREM (Aligning reads by Expectation-Maximization) is a peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  AREM

:: MORE INFORMATION

Citation:

J Comput Biol. 2011 Nov;18(11):1495-505. Epub 2011 Oct 28.
AREM: aligning short reads from ChIP-sequencing by expectation maximization.
Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X.

ASAP 0.1.2 – Align a Sequencing to two Genomes at the Same Time

ASAP 0.1.2

:: DESCRIPTION

ASAP(Allele-specific Alignment Pipeline) is a program to align a sequencing file to two genomes at the same time. This can be useful to detect allelic imbalances in samples which are of different genetic origin. Examples would be studying imprinted regions in ChIP-Seq or RNA-Seq experiments, or genomic interactions (e4C) in mouse strains with a mixed genetic background.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ASAP

:: MORE INFORMATION