Tag: Align

Sim4 20121010 – Align an Expressed DNA Sequence with a Genomic Sequence

Sim4 20121010

:: DESCRIPTION

Sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other).

::DEVELOPER

Webb Miller’s lab at the Pennsylvania State University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Sim4

:: MORE INFORMATION

Citation

Liliana Florea, George Hartzell, Zheng Zhang, Gerald M. Rubin, and Webb Miller
A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
Genome Res. 1998. 8: 967-974

ThreadPair 1.1 – Align Membrane Protein Sequences

ThreadPair 1.1

:: DESCRIPTION

ThreadPair aligns membrane protein sequences to a template of known structure. Structural information from the template is used to improve the alignment.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

 ThreadPair

:: MORE INFORMATION

Citation

Environment-Specific Substitution Tables Improve Membrane Protein Alignment
Jamie R. Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane
Bioinformatics (2011) 27 (13): i15-i23.

WAR – Webserver for Aligning structural RNAs

WAR

:: DESCRIPTION

WAR utilizes several tools simultaneously to align and predict the common secondary structure of multiple RNA sequences.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

WAR: Webserver for aligning structural RNAs
Elfar Torarinsson and Stinus Lindgreen
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W79–W84.

AGILE 0.4.0 – AliGnIng Long rEads

AGILE 0.4.0

:: DESCRIPTION

AGILE is a sequence mapping tool specifically designed to map the longer reads (read length > 200) to a given reference genome. Currently it works for 454 reads, but efforts are being made to make it suitable to work for all sequencers, which produce longer reads. Looking at the current trend of increasing read lengths, soon most of the sequencers have read lengths > 200.

::DEVELOPER

Sanchit Misra

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AGILE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):189-95. Epub 2010 Nov 18.
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.
Misra S, Agrawal A, Liao WK, Choudhary A.

M-align 2.8 – Align two time-series Microarray datasets using Time-warp or Gene-warp alignment matrices

M-align 2.8

:: DESCRIPTION

M-align is to align (non-linear resampling) the input data sets based on alignment matrices (*.ali files, see also Figure 7F) produced by Time-warp or Gene-warp programs. The alignment matrices can also be adjusted/generated manually with the account of E-maps. M-align takes as an input two matrices used to generate alignment matrix (*.ali) or two matrices with equivalent number of columns (time points) plus the alignment matrix (*.ali) itself.

::DEVELOPER

Dmitri Papatsenko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 M-align

:: MORE INFORMATION

Citation

Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.

EST_GENOME 5.2 – Align a Spliced DNA Sequence to an Unspliced Genomic Sequence

EST_GENOME 5.2

:: DESCRIPTION

est_genome is a software tool to aid the prediction of genes by sequence homology. The program will align a set of spliced nucleotide sequences (ESTs cDNAs or mRNAs) to an unspliced genomic DNA sequence, inserting introns of arbitrary length when needed. In addition, where feasible introns start and stop at the splice consensus dinucleotides GT and AG.

::DEVELOPER

Richard Mott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  EST_GENOME

:: MORE INFORMATION

Citation

Mott R.
EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA.
Comput Appl Biosci. 1997 Aug;13(4):477-8.

doublet 1.0 – Incorporate Patterns of Dipeptide Covariation to Align Protein Sequences

doublet 1.0

:: DESCRIPTION

doublet is a modified version of the Smith-Waterman algorithm that incorporates patterns of dipeptide covariation to align protein sequences.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  doublet

:: MORE INFORMATION

Citation:

Gavin A. Price, Gavin E. Crooks, Richard E. Green and Steven E. Brenner
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
Bioinformatics 21 (20): 3824-3831.

Sequoia 1.0.1 – Align Hpmologous Protein Sequences and Structures

Sequoia 1.0.1

:: DESCRIPTION

Sequoia (sequence and structure alignment) is a command-line tool for the alignment of molecular protein sequences and atomic structures. It is not exactly simulation, but it needs a stable home. I wrote it over the past 10 years, and some users have started to complain that my home server is no longer reliably available.

::DEVELOPER

Sequoia Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

  Sequoia

:: MORE INFORMATION

 

SUBOPT – Aligns Two Protein Sequences

SUBOPT

:: DESCRIPTION

SUBOPT aligns two protein sequences and can enumerate and display both optimal alignments and near optimal alignments within any distance delta of the optimal score.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 SUBOPT

:: MORE INFORMATION

Citation:

Naor, D. and Brutlag, D. L. (1994).
On Near-Optimal Alignments of Biological Sequences.
J. Computational Biology, 1(4), 349-366.

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