AIRlINER – Assessment of A-to-I RNA Editing Sites in Non-repetitive Regions

AIRlINER

:: DESCRIPTION

AIRlINER is an algorithmic approach to the assessment of A-to-I  (Adenosine-to-Inosine)  RNA editing sites in non-repetitive regions. It determines the editing probability of an adenosine by analyzing its flanking region of 10 nucleotides. Such pattern is then combined with a similar model calculated from un-edited sequences, resulting in the estimation of an unbiased editing probability.

::DEVELOPER

AIRlINER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Knowledge in the Investigation of A-to-I RNA Editing Signals.
Nigita G, Alaimo S, Ferro A, Giugno R, Pulvirenti A.
Front Bioeng Biotechnol. 2015 Feb 24;3:18. doi: 10.3389/fbioe.2015.00018.

REPPER – Detect Regions with Short Gapless REPeats in Protein Sequences

REPPER

:: DESCRIPTION

REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

M.Gruber, J. Söding , and A.N.Lupas (2005)
REPPER – repeats and their periodicities in fibrous proteins
Nucl. Acids Res., 33(2), W239-43

Pro-Coffee – Aligns Homologous Promoter Regions

Pro-Coffee

:: DESCRIPTION

Pro-Coffee is a multiple aligner specifically designed for homologous promoter regions.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Apr;40(7):e52. doi: 10.1093/nar/gkr1292. Epub 2012 Jan 9.
Use of ChIP-Seq data for the design of a multiple promoter-alignment method.
Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C.

REX – Region Evolution eXplorer

REX

:: DESCRIPTION

REX is a web-based system for exploring the evolution of ontology parts (regions).

::DEVELOPER

Interdisciplinary Centre for Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Region Evolution eXplorer – A tool for discovering evolution trends in ontology regions.
Christen V, Hartung M, Groß A.
J Biomed Semantics. 2015 Jun 1;6:26. doi: 10.1186/s13326-015-0020-6. eCollection 2015.

GISTIC 2.0.22 – Detect Regions of Significant Copy-number Gains and Losses

GISTIC 2.0.22

:: DESCRIPTION

GISTIC  (Genomic Identification of Significant Targets in Cancer) facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISTIC

:: MORE INFORMATION

Citation

Genome Biol. 2011;12(4):R41. Epub 2011 Apr 28.
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G.

BamReadCount 0.01 – Calculate Read Count for each region in the input list of Regions

BamReadCount 0.01

:: DESCRIPTION

The tool BamReadCount calculates the number of reads covering a list of input regions and the normalized read count w.r.t total mapped reads and region length. It also outputs the GC content of each region and the associated read count in the corresponding GC bin, which will be used for correcting the GC bias.

::DEVELOPER

Computational Genetics and Genomics Lab, Vanderbilt University School of Medicine.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

  BamReadCount

:: MORE INFORMATION

pfilt 1.5 – Sequence Filtering for Low-complexity, Coiled-coil and Biased Amino Acid Regions

pfilt 1.5

:: DESCRIPTION

pfilt program is designed to mask out (i.e. replace amino acid characters with Xs) regions of low complexity, coiled-coil regions and regions with extremely biased amino acid compositions. For compositional biased regions,only the overrepresented amino acids are masked.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  pfilt

:: MORE INFORMATION

Citation:

Jones, D.T. & Swindells, M.B. (2002)
Getting the most from PSI-BLAST.
Trends Biochem Sci. 2002 Mar;27(3):161-4.

DiNuP 1.3 – Identify Regions of Differential Nucleosome Positioning

DiNuP 1.3

:: DESCRIPTION

DiNuP compares the nucleosome profiles generated by high-throughput sequencing between different conditions. DiNuP provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise. Evaluation of DiNuP showed it to be both sensitive and specific for the detection of changes in nucleosome location, occupancy and fuzziness. RDNPs that were identified using publicly available datasets revealed that nucleosome positioning dynamics are closely related to the epigenetic regulation of transcription.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  DiNuP

:: MORE INFORMATION

Citation

Fu K, Tang Q, Feng J, Liu XS, Zhang Y.
DiNuP: a systematic approach to identify regions of differential nucleosome positioning.
Bioinformatics 2012; 28(15):1965-71.

RegionalHapMapExtractor – Extract a Region from HapMapII for MaCH imputation

RegionalHapMapExtractor

:: DESCRIPTION

RegionalHapMapExtractor is a software to extract a region from hapMapII for MaCH imputation

::DEVELOPER

Yun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Perl
:: DOWNLOAD

 RegionalHapMapExtractor

:: MORE INFORMATION

Spotter 0.5 – Identify Region of Interest near Associated Variant

Spotter 0.5

:: DESCRIPTION

Spotter is a program for identifying a region of interest (using LD and recombination) near an associated variant.

::DEVELOPER

Ryan Welch (welchr@umich.edu) at the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Spotter

 

:: MORE INFORMATION

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