mSD – Regulatory Module Identification

mSD

:: DESCRIPTION

mSD (motif-guided sparse decomposition) identifies gene regulatory modules by integrating gene expression data and DNA sequence motif information. The mSD approach is implemented as a two-step algorithm comprising estimates of (1) transcription factor activity and (2) the strength of the predicted gene regulation event(s).

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mSD

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Mar 22;12:82.
Motif-guided sparse decomposition of gene expression data for regulatory module identification.
Gong T, Xuan J, Chen L, Riggins RB, Li H, Hoffman EP, Clarke R, Wang Y.

BreakSeq 1.3 – Structural Variants Annotation and Identification pipeline

BreakSeq 1.3

:: DESCRIPTION

BreakSeq is a pipeline for annotation, classification and analysis of Structural Variants (SVs) at single nucleotide resolution

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BreakSeq

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2010 Jan;28(1):47-55. Epub 2009 Dec 27.
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.
Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB.

IDEG 6.2 – Identification of Differentially Expressed Genes in Multiple Tag Sampling Experiments

IDEG 6.2

:: DESCRIPTION

IDEG allows identification of differentially expressed genes by statistical analysis of large matrices of multiconditional expression data (ESTs or SAGE tags counts), the selection of different test statistics, possibly with Bonferroni correction and the display of result tables, linked to the GenBank, UniGene or LocusLink database.

::DEVELOPER

COMPUTATIONAL GENOMICS LABORATORY, Department of Biology, University of Padova, Italy.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IDEG

:: MORE INFORMATION

Citation:

Chiara Romualdi , Stefania Bortoluzzi , Fabio d’Alessi and Gian Antonio Danieli
IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments.
PHYSIOL GENOMICS. 2003; 12(2): 159-62

cBar 1.2 – Identification of Chromosomal Sequence Fragments from Metagenome data

cBar 1.2

:: DESCRIPTION

cBar is a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 cBar

:: MORE INFORMATION

Citation

Fengfeng Zhou, Ying Xu
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
Bioinformatics, 2010 26(16):2051-2052.

KOBAS 2.0 – Annotation and Identification of Enriched Pathways and Diseases

KOBAS 2.0

:: DESCRIPTION

KOBAS  (KEGG Orthology Based Annotation System) is a web server that annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases.

::DEVELOPER

KOBAS Team

:: REQUIREMENTS

:: DOWNLOAD

 KOBAS

:: MORE INFORMATION

Citation

Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C. and Wei, L. (2011)
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.
Nucleic Acids Res, 39, W316-322

ONCOR 20080424 – Genetic Stock Identification

ONCOR 20080424

:: DESCRIPTION

ONCOR is a computer program useful for genetic mixture analysis and assignment tests. These are genetic tests for identifying the origin of individuals sampled in a mixture of individuals from genetically distinct populations.

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 ONCOR

:: MORE INFORMATION

Citation

Anderson EC, RS Waples, ST KALINOWSKI (2007).
An improved method for estimating the accuracy of genetic stock identification.
Canadian Journal of Fisheries and Aquatic Sciences

GBIRP – Genotype-Based Identification of Relative Pairs

GBIRP

:: DESCRIPTION

GBIRP ( Genotype-Based Identification of Relative Pairs)is a program to compare the genotypes of many pairs of people, and identify pairs of people who may be related to each other.

::DEVELOPER

Jim Stankovich (stankovich@wehi.edu.au) @ WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GBIRP

:: MORE INFORMATION

Citation:

Hum Genet. 2005 Jul;117(2-3):188-99
Identifying nineteenth century genealogical links from genotypes.
Stankovich J, Bahlo M, Rubio JP, Wilkinson CR, Thomson R, Banks A, Ring M, Foote SJ, Speed TP.

PrimerHunter 1.0.2 – Primer Design for PCR-Based Virus Subtype Identification

PrimerHunter 1.0.2

:: DESCRIPTION

PrimerHunter is a tool for selecting highly sensitive and specific primers for virus subtyping. It takes as input sets of both target and non-target sequences and ensures that selected primers amplify all target sequences and none of the non-target sequences by relying on accurate melting temperature computations based on the nearest-neighbor model of Santalucia and the fractional programming algorithm of  Leber et al.

PrimerHunter Online version

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PrimerHunter

:: MORE INFORMATION

Citation:

J. Duitama and D.M. Kumar and E. Hemphill and M. Khan and I.I. Mandoiu and C.E. Nelson,
PrimerHunter: A Primer Design Tool for PCR-Based Virus Subtype Identification,
Nucleic Acids Research 37, pp. 2483-2492, 2009

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