Tag: Genomic Sequence

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

GenRGenS 2.1 – Generation of Random Genomic Sequences and Structures

GenRGenS 2.1

:: DESCRIPTION

GenRGenS is a software dedicated to random generation of genomics sequences that supports several classes of models, including Markov chains, HMM, context-free grammars, PROSITE patterns and more.

::DEVELOPER

GenRGenS Team 

:: SCREENSHOTS

GenRGenS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 GenRGenS

:: MORE INFORMATION

Citation

Y. Ponty, M. Termier and A. Denise [pdf] [bib]
GenRGenS: Software for generating random genomic sequences and structures
Bioinformatics, June 2006 22(12):1534-1535.

Nucleosomes Positioning 3.0 – Prediction by Genomic Sequence

Nucleosomes Positioning 3.0

:: DESCRIPTION

Nucleosomes Positioning allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model.

::DEVELOPER

Segal Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Nucleosomes Position

:: MORE INFORMATION

Citation

Kaplan et al.,
“The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome“,
Nature 458, 362-366

FastaGrep 2.0 – Search Oligonucleotide Binding Sites from FastA Genomic Sequences

FastaGrep 2.0

:: DESCRIPTION

FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. It can do both, match/mismatch based and thermodynamic binding energy searches.

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastaGrep

:: MORE INFORMATION

SIBsim4 0.20 – Align an Expressed DNA Sequence with a Genomic Sequence based Sim4

SIBsim4 0.20

:: DESCRIPTION

SIBsim4 project is based on sim4, which is a program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns.

::DEVELOPER

The SIB Swiss Institute of Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SIBsim4

:: 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

RAT 1.0 – Recombination Analysis Tool for High Throughput Analysis of Genomic Sequence

RAT 1.0

:: DESCRIPTION

RAT (Recombination Analysis Tool)is an uncomplicated and intuitive cross-platform Java-based application intended for high-throughput, distance-based analysis of both DNA and protein multiple sequence alignments, in any one of seven different file formats. All of RAT’s operations are carried out through GUI’s, and all output can be saved as data files (.txt, .xls, .csv), or .jpg files in the case of graphical outputs. RAT is intuitive and easy to use, and only requires a minimum of input from the user. All the parameters have default values, all of which may be changed by the user.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

  RAT 

:: MORE INFORMATION

Citation:

Etherington GJ, Dicks J and Roberts IN (2005)
Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination.
Bioinformatics 21(3):278-281.

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