Tag: Genomic

pgltools 2.2.0 – Paired Genomic Loci Tool Suite

pgltools 2.2.0

:: DESCRIPTION

Pgltools is a genomic arithmetic software suite designed for working with paired-loci genomic data, such as contacts from a Hi-C or ChIA-PET experiment, and utilizes the PGL file format.

::DEVELOPER

frazer Lab, UCSD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Pgltools

:: MORE INFORMATION

Citation

Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA.
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.
BMC Bioinformatics. 2017 Apr 7;18(1):207. doi: 10.1186/s12859-017-1621-0. PMID: 28388874; PMCID: PMC5384132.

genomation 0.99.7 – R package for Graphics and Operations for Genomic

genomation 0.99.7

:: DESCRIPTION

Genomation is an R package for genomic feature analysis and annotation by extending bioconductor packages.

::DEVELOPER

BIMSB bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 genomation

:: MORE INFORMATION

Citation

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin A, Franke V, Vlahoviček K, Mason CE, Schübeler D.
Bioinformatics. 2014 Nov 21. pii: btu775.

ProSplign 20170203 – Alignment of Proteins against Genomic Sequences

ProSplign 20170203

:: DESCRIPTION

ProSplign is a global alignment tool developed by Dr. Boris Kiryutin. It produces accurate spliced alignments and locates alignments of distantly related proteins with low similarity.

::DEVELOPER

Dr. Boris Kiryutin (kiryutin@ncbi.nlm.nih.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ProSplign

:: MORE INFORMATION

Citation

ProSplign – Protein to Genomic Alignment Tool.
B. Kiryutin, A. Souvorov, T. Tatusova.
Manuscript in preparation

GNUMAP 3.0.2 – Genomic Next-generation Universal MAPper

GNUMAP 3.0.2

:: DESCRIPTION

The GNUMAP (Genomic Next-generation Universal MAPper) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. Currently, gnumap is designed to be used with the _int.txt data received from the Solexa/Illumina machine.

::DEVELOPER

GNUMAP Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GNUMAP

:: MORE INFORMATION

Citation:

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
Bioinformatics (2010) 26 (1): 38-45.

GPKB – Genomic and Proteomic Knowledge Base

GPKB

:: DESCRIPTION

GPKB integrates several of the most relevant sources of such dispersed information (including Entrez Gene, UniProt, IntAct, Expasy Enzyme, GO, GOA, BioCyc, KEGG, Reactome, and OMIM).

::DEVELOPER

GPKB team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Masseroli M, Canakoglu A, Ceri S.
Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction.
IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar-Apr;13(2):209-19. doi: 10.1109/TCBB.2015.2453944. PMID: 27045824.

RIPCAL 2.0 – Analysis of RIP in Fungal Genomic DNA Repeats

RIPCAL 2.0

:: DESCRIPTION

RIPCAL is a bioinformatics tool for the analysis of repeat-induced point mutation (RIP) of fungi.

::DEVELOPER

Dr James Hane

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl
:: DOWNLOAD

 RIPCAL

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:655. doi: 10.1186/1471-2164-11-655.
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes.
Hane JK1, Oliver RP.

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.
Hane JK, Oliver RP.
BMC Bioinformatics. 2008 Nov 12;9:478. doi: 10.1186/1471-2105-9-478.

GNomEx – Genomic Experimental Data Repository and Core LIMS

GNomEx

:: DESCRIPTION

GNomEx provides a web accessible database and LIMS to organize and track the generation of raw genomic data, its associated downstream analysis, and to programmatically distribute the data to client applications such as IGB and the UCSC Genome Browser.

::DEVELOPER

The Bioinformatics Shared Resource

:: SCREENSHOTS

GNomEx

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 GNomEx

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Sep 9;11:455. doi: 10.1186/1471-2105-11-455.
Next generation tools for genomic data generation, distribution, and visualization.
Nix DA1, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ.

Splign 20150223 – Compute cDNA-to-Genomic / Spliced Sequence Alignment

Splign 20150223

:: DESCRIPTION

Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm which identifies possible gene duplications, and a refined alignment algorithm recognizing introns and splice signals.

Splign Online Version

::DEVELOPER

NCBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

Splign

:: MORE INFORMATION

Citation

Y.Kapustin, A.Souvorov, T.Tatusova and D.Lipman.
Splign: algorithms for computing spliced alignments with identification of paralogs.
Biology Direct, May 2008.

Dintor – Functional Annotation of Genomic and Proteomic data

Dintor

:: DESCRIPTION

Dintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets.

::DEVELOPER

the Center of Biomedicine (CBM)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Dintor

:: MORE INFORMATION

Citation

Dintor: functional annotation of genomic and proteomic data.
Weichenberger CX, Blankenburg H, Palermo A, D’Elia Y, K?nig E, Bernstein E, Domingues FS.
BMC Genomics. 2015 Dec 21;16(1):1081. doi: 10.1186/s12864-015-2279-5.

BISQUE 1.0 – a human Genomic, Proteomic, and Transcriptomic Conversion tool

BISQUE 1.0

:: DESCRIPTION

BISQUE (The Biological Sequence Exchange) is a bioinformatics tool enabling locus and variant-specific conversion among human gene, transcript, and protein identifiers from several popular databases.

::DEVELOPER

Yu Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  BISQUE

:: MORE INFORMATION

Citation

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic, and proteomic database identifiers.
Meyer MJ, Geske P, Yu H.
Bioinformatics. 2016 Jan 23. pii: btw043.