Tag: Genome

MuMRescueLite 20090522 – Use the Tag Sequencies of mapped to Multiple Loci to the Genome

MuMRescueLite 20090522

:: DESCRIPTION

MuMRescueLite is the software that enable to use the tag sequencies of mapped to multiple loci to the genome, for the expression analysis. At the mapping of short sequence tags of CAGE or ChIP-Seq to the genome, sequence tags that map to multiple genomic loci (multi-mapping tags or MuMs), are routinely omitted from further analysis, leading to experimental bias and reduced coverage.

::DEVELOPER

Takehiro Hashimoto, Michiel J. L. deHoon, Geoffrey J. Faulkner

:: SCREENSHOTS

N/A

::  REQUIREMENTS

  • Linux / MacOSX / Windows
  • Python

:: DOWNLOAD

  MuMRescueLite

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 1;25(19):2613-4. Epub 2009 Jul 15.
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
Hashimoto T, de Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ.

 

ASAP 1.4.1 – A Systematic Annotation Package for Community Analysis of Genomes

ASAP 1.4.1

:: DESCRIPTION

ASAP is designed to organize the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization, providing a vehicle for ongoing updates of the annotation and a repository for genome-scale experimental data. Development was motivated by the need to more directly involve a greater community of researchers, with their collective expertise, in keeping the genome annotation current and to provide a synergistic link between up-to-date annotation and functional genomic data.

::DEVELOPER

Genome Evolution Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • PHP
  • MySQL

:: DOWNLOAD

 ASAP

:: MORE INFORMATION

Citation:

ASAP, a systematic annotation package for community analysis of genomes.
Glasner JD, Liss P, Plunkett G 3rd, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT.
Nucleic Acids Res. 2003 Jan 1;31(1):147-51.

MPscan – Index free Mapping of multiple short reads on a Genome

MPscan

:: DESCRIPTION

The program mpscan (Multi Pattern Scanner) is a software that performs Set Pattern Matching on nucleotitic sequences (DNA/RNA): it searches for a large set of patterns at once in a sequence.

::DEVELOPER

Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 MPscan

:: MORE INFORMATION

Citation

Rivals E., Salmela L., Kiiskinen P., Kalsi P., Tarhio J.
mpscan: Fast Localisation of Multiple Reads in Genomes
Lecture Notes in BioInformatics (LNBI), Springer-Verlag, Vol. 5724, p. 246-260, 2009.

REEF – Search REgionally Enriched Features in Genomes

REEF

:: DESCRIPTION

REEF (REgionally Enriched Features) is a tool that uses a genome scan method in order to find chromosomal regions in which a specific features class is enriched. A feature class may be based on whatever sequence characteristics. For instance, it may consist of a class of genes, defined by analysis of gene expression or by involvement of gene products in specific pathways or interaction groups.

::DEVELOPER

Human Genetics, Bioinformatics and Computational Genomics Group , Biology Department, Padova University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 REEF

:: MORE INFORMATION

Citation:

Coppe A., Danieli G.A. and Bortoluzzi S.
REEF: searching REgionally Enriched Features in genomes.
BMC BIOINFORMATICS. 7: 453.

Tagger 1.3 – Genome/Transcriptome-wide Tag Scanner

Tagger 1.3

:: DESCRIPTION

Tagger is a tool which allows searching fixed-sequence tags (or sequence branches) against entire genomes or mRNA reference sequence databases.

TanScan Online

::DEVELOPER

Computational Cancer Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Tagger

:: MORE INFORMATION

Citation

Indexing Strategies for Rapid Searches of Short Words in Genome Sequences
Iseli C, Ambrosini G, Bucher P, and Jongeneel CV.
PLoS ONE. 2007; 2(6): e579.

ComPhy – Genome Composite Distance Phylogeny for whole-genome phylogeney inferences

ComPhy

:: DESCRIPTION

ComPhy (Genome Composite Distance Phylogeny)  is a java based tool for whole-genome gene set phylogeney inferences.The software determines a prokaryotic phylogeny by calculating a composite distance based on the comparison of complete gene sets between two genomes. It does not require multiple sequence alignment and is fully automated. The composite distance between two genomes is defined by three components: Gene Dispersion Distance (GDD), Gene Content Distance (GCD), and Genome Breakpoint-based Distance (GBD). GDD quantifies the dispersion of ortholog clusters along the genomic coordinates from one genome to another; GCD measures the level of shared orthologs between two genomes; GBD measures the shared break-points between two genomes. The phylogenetic tree is constructed using a neighbour joining method using Phylip from the distance matrix calculated by the composite distance. ComPhy also provides the performance measure of the generated tree against Bergey’s taxonomy system.

::DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 ComPhy

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S5.
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.
Lin GN, Cai Z, Lin G, Chakraborty S, Xu D.

CAP3 / PCAP – Sequence and Genome Assembly Programs

CAP3 / PCAP

:: DESCRIPTION

CAP3 is a sequence assembly program for small-scale assembly of EST sequences with or without quality values.

PCAP is for large-scale assembly of genomic sequences with quality values and with or without forward-reverse read pairs.

::DEVELOPER

Xiaoqiu Huang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 CAP3 / PCAP

:: MORE INFORMATION

Citation:

Huang, X. and Madan, A. (1999)
CAP3: A DNA Sequence Assembly Program.
Genome Research, 9: 868-877.

Huang, X., Wang, J., Aluru, S., Yang, S.-P. and Hillier, L. (2003)
PCAP: A Whole-Genome Assembly Program.
Genome Research, 13: 2164-2170.

Restauro-G 1.0 – Genome Re-Annotation System for Comparative Genomics

Restauro-G 1.0

:: DESCRIPTION

Restauro-G is an open-source rapid genome re-annotation software system , specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases

::DEVELOPER

Satoshi Tamaki
Kazuharu Arakawa

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Restauro-G 

:: MORE INFORMATION

Citation

Satoshi Tamaki, Kazuharu Arakawa*, Nobuaki Kono, and Masaru Tomita.
“Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics”
Genomics Proteomics Bioinformatics. 2007 Feb;5(1):53-8.

Pairagon 1.1 – Pair-HMM based cDNA-to-genome Alignment

Pairagon 1.1

:: DESCRIPTION

Pairagon is a pair-HMM based cDNA-to-genome alignment program.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Pairagon

:: MORE INFORMATION

Citation

Lu D.V., Brown R.H., Arumugam M., Brent M.R.. 2009.
“Pairagon: A Highly Accurate, HMM-based cDNA-to-genome Aligner.”
Bioinformatics 25 (13): 1587-1593.

Murasaki 1.68.6 – Find Anchors from Multiple Genomes

Murasaki 1.68.6

:: DESCRIPTION

Murasaki provides an open source platform to take advantage of long patterns, cluster computing, and novel hash algorithms to produce accurate anchors across multiple genomes with computational efficiency significantly greater than existing methods.

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Murasaki

:: MORE INFORMATION

Citation:

Kris Popendorf, Hachiya Tsuyoshi, Yasunori Osana, Yasubumi Sakakibara
Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes
PLoS ONE 5(9): e12651.

Exit mobile version