Patser v3e – Find Locations of Patterns in Sequence

Patser v3e

:: DESCRIPTION

Patser scores the L-mers (subsequences of length L) of the indicated sequences against the indicated alignment or weight matrix.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CCompiler

:: DOWNLOAD

 Patser

:: MORE INFORMATION

SRF 1.1 – Find Repeats through an analysis of the power Spectrum of a given DNA Sequence

SRF 1.1

:: DESCRIPTION

 SRF (Spectral Repeat Finder) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. SRF is an ab initio technique as no prior assumptions need to be made regarding either the repeat length, its fidelity, or whether the repeats are in tandem or not

::DEVELOPER

SRF Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Jun 12;20(9):1405-12. Epub 2004 Feb 19.
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation.
Sharma D, Issac B, Raghava GP, Ramaswamy R.

PhiSpy 2.3 – Find Prophages in Microbial Genomes

PhiSpy 2.3

:: DESCRIPTION

PhiSpy is a novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PhiSpy

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep;40(16):e126. doi: 10.1093/nar/gks406. Epub 2012 May 14.
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies.
Akhter S1, Aziz RK, Edwards RA.

LBL 1.0 / LBLGXE 1.1 – Bayesian Lasso for detecting Rare Haplotype-Environment Interaction

LBL 1.0 / LBLGXE 1.1

:: DESCRIPTION

LBL (Logistic Bayesian Lasso) is an R package that performs Logistic Bayesian Lasso for finding association of SNP haplotypes with a trait in a case-control setting. Bayesian lasso is used to find the posterior distributions of logistic regression coefficients, which are then used to calculate Bayes Factor to test for association with haplotypes.

LBLGXE expands on the original LBL. Gene-environment interaction (GXE)

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LBL / LBLGXE

:: MORE INFORMATION

Citation

Genet Epidemiol. 2014 Jan;38(1):31-41. doi: 10.1002/gepi.21773. Epub 2013 Nov 23.
Detecting rare haplotype-environment interaction with logistic Bayesian LASSO.
Biswas S1, Xia S, Lin S.

Biswas S, and Lin, S. (2011)
Logistic Bayesian Lasso for identifying association with rare haplotyp es and application to age-related macular degeneration.
Biometrics. 2011 Sep 28. doi: 10.1111/j.1541-0420.

FOOTER 2.0 – Find Ammalian Transcription Factor Binding Sites using Phylogenetic Footprinting

FOOTER 2.0

:: DESCRIPTION

FOOTER analyses a pair of homologous mammalian DNA sequences (i.e. human and mouse/rat) for high probability binding sites of known transcription factors. A set of Position-Specific Scoring Matrices (PSSM) has been carefully constructed from mammalian transcription factor binding sites deposited in TRANSFAC database.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.
Corcoran DL, Feingold E, Benos PV.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.

FIND 0.31 – Flow Investigation using N-Dimensions

FIND 0.31

:: DESCRIPTION

FIND is a software package designed to facilitate the visualization and analysis of Flow Cytometry data for the scientific target audience, as well as providing a target platform for developers to implement their FC-specific algorithms.

::DEVELOPER

Battelle Center for Mathematical Medicine

:: SCREENSHOTS

find

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 FIND

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 10;12:145. doi: 10.1186/1471-2105-12-145.
FIND: a new software tool and development platform for enhanced multicolor flow analysis.
Dabdoub SM1, Ray WC, Justice SS.

CleaveLand 4.3 – Find Cleaved Small RNA Targets

CleaveLand 4.3

:: DESCRIPTION

CleaveLand is a command-line executed pipeline for finding cleaved small RNA targets using degradome data (also known as PARE [parallel analysis of RNA ends] and GMUCT [genome-wide mapping of uncapped transcripts]).  Provided with a set of degradome data, a list of small RNA queries, a reference transcriptome/mRNA set, CleaveLand outputs potentially cleaved small RNA targets along with other supporting information.

::DEVELOPER

Axtell Lab @ Penn State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CleaveLand

:: MORE INFORMATION

Citation:

Addo-Quaye, C., Miller, W., and Axtell, M.J. (2009).
CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets.
Bioinformatics 25: 130-131.

DisLocate – Find Disulfide bonds in Eukaryotes with predicted subcellular Localization

DisLocate

:: DESCRIPTION

 DisLocate is a a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No. Only Web Service

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2224-30. Epub 2011 Jun 29.
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
Savojardo C, Fariselli P, Alhamdoosh M, Martelli PL, Pierleoni A, Casadio R.

SnowShoes-FTD – Find Fusions from RNA-Seq data

SnowShoes-FTD

:: DESCRIPTION

SnowShoes-FTD is a bioinformatics tool to identify fusion transcripts from paired-end transcriptome sequencing data. The tool employs multiple steps of false positive filtering and nominates the fusion candidates with high confidence (approaching 100% true positive rate). The unique features of SnowShoes-FTD include: (i) the ability to discover multiple fusion isoforms in which the two gene partners give rise to transcripts with different junctions; (ii) prediction of potential fusion mechanisms including inversion, translocation, and/or interstitial deletions; (iii) identification of whether the junction point in a fusion transcript occurs at the boundaries of known exons which implies the fusion events might have happened inside an intron in DNA and transcribed to the fusion transcript.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Please contact the author, Yan W. Asmann, Ph.D. smann.yan@mayo.edu

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 Aug;39(15):e100. Epub 2011 May 27.
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.

SatFind – C-program for Finding Satellites in Genomes

SatFind

:: DESCRIPTION

SatFind – C-program for Finding Satellites in Genomes

::DEVELOPER

 the Algorithmics and Genetics Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C compiler

:: DOWNLOAD

 SatFind

:: MORE INFORMATION

Citation

PLoS One. 2013 Apr 24;8(4):e62221. doi: 10.1371/journal.pone.0062221.
A satellite explosion in the genome of holocentric nematodes.
Subirana JA, Messeguer X.