UnMeRFi – Under-Methylated Region Finder

UnMeRFi

:: DESCRIPTION

UnMeRFi (Under-Methylated Region Finder) estimates under-methylated regions in an unspecified DNA sequence. The program works by using a moving window (the size of which can be specified by the user) and by assessing the likelihood of that window to be under-methylated. As a final step windows passing the threshold  are joined to form contiguous under-methylated regions.

::DEVELOPER

Yakhini Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 UnMeRFi

:: MORE INFORMATION

Citation

Straussman et al
Developmental programming of CpG island methylation profiles in the human genome
Nature Structural & Molecular Biology 16, 564 – 571 (2009)

CLEVER Toolkit 2.4 – Clique Enumerating Variant Finder

CLEVER Toolkit 2.4

:: DESCRIPTION

The CLEVER Toolkit (CTK) is a collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads.

::DEVELOPER

The CWI Life Sciences and Health (LSH) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C++ Compiler
  • Python 

:: DOWNLOAD

CLEVER Toolkit

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Nov 15;28(22):2875-82. doi: 10.1093/bioinformatics/bts566. Epub 2012 Oct 11.
CLEVER: clique-enumerating variant finder.
Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A.

ESEfinder 3.0 – Exon Splicing Enhancer Finder

ESEfinder 3.0

:: DESCRIPTION

ESEfinder is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

::DEVELOPER

ESEfinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Smith, P. J., Zhang, C., Wang, J. Chew, S. L., Zhang, M. Q. and Krainer, A. R. 2006.
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers.
Hum. Mol. Genet. 15(16): 2490-2508.

Cartegni L., Wang J., Zhu Z., Zhang M. Q., Krainer A. R.; 2003.
ESEfinder: a web resource to identify exonic splicing enhancers.
Nucleic Acid Research, 2003, 31(13): 3568-3571.

ExonHunter 1.07 – Comparative Gene Finder

ExonHunter 1.07

:: DESCRIPTION

ExonHunter is a comprehensive gene finder based on hidden Markov models allowing use of variety of additional sources of information (ESTs, proteins, genome-genome comparison, repeats, and more).

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 ExonHunter

:: MORE INFORMATION

Citation

ExonHunter: a comprehensive approach to gene finding.
Brejová B, Brown DG, Li M, Vinar T.
Bioinformatics. 2005 Jun;21 Suppl 1:i57-65.

JAMM 1.0.7rev3 – Peak Finder for NGS Datasets

JAMM 1.0.7rev3

:: DESCRIPTION

JAMM (Joint Analysis of NGS replicates via Mixture Model clustering)is a peak finder for NGS datasets that can integrate replicates and assign peak boundaries accurately.

::DEVELOPER

JAMM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 JAMM

:: MORE INFORMATION

Citation:

JAMM: A Peak Finder for Joint Analysis of NGS Replicates.
Ibrahim MM, Lacadie SA, Ohler U.
Bioinformatics. 2014 Sep 15. pii: btu568.

TRF 4.09 – Tandem Repeats Finder

TRF 4.09

:: DESCRIPTION

TRF (Tandem Repeats Finder) is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. There is no need to specify the pattern, the size of the pattern or any other parameter. The output consists of two files: a repeat table file and an alignment file. The repeat table contains information about each repeat, including its location, size, number of copies and nucleotide content. Clicking on the location indices for one of the table entries opens a second web browser that shows an alignment of the copies against a consensus pattern. The program is very fast, analyzing sequences on the order of .5Mb in just a few seconds. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected. Sequence information sent to the server is confidential and deleted after program execution.

::DEVELOPER

Gary Benson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

  TRF

:: MORE INFORMATION

Citation:

G. Benson,
Tandem repeats finder: a program to analyze DNA sequences
Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.

IRF 3.07 – Inverted Repeats Finder

IRF 3.07

:: DESCRIPTION

IRF(Inverted Repeats Finder) investigate inverted repeat structure of the Human Genome

::DEVELOPER

Laboratory for Biocomputing and Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 IRF

:: MORE INFORMATION

Citation:

P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson.
Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes” ,
Genome Research, 14:1861-1869, 2004.

UPF 0.911 – Unique Peptide Finder

UPF 0.911

:: DESCRIPTION

UPF is used to calculate sets of unique peptides from protein sequences. Furthermore, UPF provides the possibility to calculate both the frequency of peptides and to retrieve information from which proteins a particular peptide can be derived.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

upf

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 UPF

:: MORE INFORMATION

FusionCatcher 0.99.3e – Fusion Genes Finder for RNA-seq data

FusionCatcher 0.99.3e

:: DESCRIPTION

FusionCatcher searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

::DEVELOPER

Kallioniemi Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • Biopyton
  • Bowtie

:: DOWNLOAD

 FusionCatcher

:: MORE INFORMATION

Citation

S. Kangaspeska, S. Hultsch, H. Edgren, D. Nicorici, A. Murumägi, O.P. Kallioniemi,
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms,
PLoS ONE 7(10): e48745. doi:10.1371/journal.pone.0048745

HUF-ZINC – HMM-based U-shape Motif Finder for Zinc Binding

HUF-ZINC

:: DESCRIPTION

HUF-ZINC is a HMM-based web server for prediction of the novel, as well as conventional, zinc finger motifs in protein sequences.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340008. doi: 10.1142/S0219720013400088. Epub 2013 Jan 16.
Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding (“Huf-Zinc”) motif.
Maurer-Stroh S1, Gao H, Han H, Baeten L, Schymkowitz J, Rousseau F, Zhang L, Eisenhaber F.