Tag: GAP

GAP 2009 – Mining complex Cancer Genomic Profiles

GAP 2009

:: DESCRIPTION

GAP (Genome Alteration Print) is a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

::DEVELOPER

Tatiana Popova, Institut Curie, Paris

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX
  • R package

:: DOWNLOAD

 GAP

:: MORE INFORMATION

Citation

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.
Popova T, Manié E, Stoppa-Lyonnet D, Rigaill G, Barillot E, Stern MH.
Genome Biol. 2009;10(11):R128. doi: 10.1186/gb-2009-10-11-r128.

AGapEs – Gap filling based on Template Sequence for aDNA data

AGapEs

:: DESCRIPTION

AGapEs (ancestral gap estimation) is an optimization-based mathod to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AGapEs

:: MORE INFORMATION

Citation

Luhmann N, Doerr D, Chauve C.
Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.
Microb Genom. 2017 Jul 8;3(9):e000123. doi: 10.1099/mgen.0.000123. PMID: 29114402; PMCID: PMC5643016.

FGAP 1.8.1 – Automated Gap Closing tool

FGAP 1.8.1

:: DESCRIPTION

FGAP aims to improve genome sequences by merging alternative assemblies or incorporating alternative data, analyzing the gap region and indicating the best sequence to close the gap.

::DEVELOPER

Vitor C. Piro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • MatLab

:: DOWNLOAD

 FGAP

:: MORE INFORMATION

Citation

BMC Res Notes. 2014 Jun 18;7:371. doi: 10.1186/1756-0500-7-371.
FGAP: an automated gap closing tool.
Piro VC, Faoro H, Weiss VA, Steffens MB, Pedrosa FO, Souza EM, Raittz RT

GAP – Distinguishing between Amyloid Fibril-forming and Amorphous β-aggregating Aggregation-prone Regions

GAP

:: DESCRIPTION

GAP (Generalized Aggregation Proneness) distinguishes between amyloid fibril-forming and amorphous β-aggregating hexapeptides with almost 100 percent accuracies in validation tests performed using non-redundant datasets.

::DEVELOPER

GAP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 15;30(14):1983-90. doi: 10.1093/bioinformatics/btu167. Epub 2014 Mar 28.
GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies.
Thangakani AM, Kumar S, Nagarajan R, Velmurugan D, Gromiha MM.

GAP 0.0.1 – Gene functional Association Predictor

GAP 0.0.1

:: DESCRIPTION

GAP is an integrative, general-purpose framework for deriving a quantitative measure of gene similarity, which is relevant to a wide range of bioinformatics applications from gene clustering and phenotype and protein interactions predictions to interaction network modeling, and pharmacology analysis.

::DEVELOPER

Jurisica Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Mar 14;7:22. doi: 10.1186/1752-0509-7-22.
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations.
Vafaee F, Rosu D, Broackes-Carter F, Jurisica I.

Mac5 1.7.3 – Phylogenetic Reconstruction using Gapped Data

Mac5 1.7.3

:: DESCRIPTION

MAC5 is a program which implements MCMC sampling to estimate a phylogenetic tree from a DNA multiple alignment. What differentiates MAC5 from similar programs (e.g. BAMBE, MrBayes) is its use of five-state sequence evolution models as a means to include the gap information when estimating an alignment. Despite vilification of these models in the literature in the past (e.g., Durbin et al., 1998, p. 217), we have found that, in many circumstances, they are useful for improving the precision of topology estimation.

::DEVELOPER

Grainne McGuire and Paul-Michael Agapow

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 MAC5

:: MORE INFORMATION

Citation:

Gráinne McGuire, Michael C. Denham and David J. Balding
MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gaps
Bioinformatics (2001) 17 (5): 479-480.

GapFiller 2.1.2 – Closing the Gap within Paired Reads

GapFiller 2.1.2

:: DESCRIPTION

GapFiller is not a standard de novo assembler. It aims “only” at closing the gap between pairs of reads as a first step of a large number of downstream analysis

::DEVELOPER

Francesca Nadalin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GapFiller

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.
GapFiller: a de novo assembly approach to fill the gap within paired reads.
Nadalin F1, Vezzi F, Policriti A.

GMcloser 1.6.2 / GMvalue 1.3 – Closing the Gaps in Scaffolds with Preassembled Contigs

GMcloser 1.6.2 / GMvalue 1.3

:: DESCRIPTION

GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.

GMvalue is a tool to determine misassembly sites in contigs and scaffolds.

::DEVELOPER

GMcloser team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GMcloser / GMvalue

:: MORE INFORMATION

Citation

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments.
Kosugi S, Hirakawa H, Tabata S.
Bioinformatics. 2015 Aug 10. pii: btv465.

GAP 1.2.14 – Geometric Analysis of Proteins

GAP 1.2.14

:: DESCRIPTION

GAP (Geometric Analysis Programs)   contains two separate program packages that were developed in parallel for the generation and analysis of structure ensembles.

::DEVELOPER

G.P. Gippert

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window with Cygwin / Linux / Mac OsX

:: DOWNLOAD

GAP

:: MORE INFORMATION