Tag: Genome

COGs 201204 – Phylogenetic Classification of Proteins encoded in complete Genomes

COGs 201204

:: DESCRIPTION

COGs (Collections of Clusters of Orthologous Genes) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes.

::DEVELOPER

National Center for Biotechnology Information

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 COGs

:: MORE INFORMATION

Citation

Biol Direct. 2012 Dec 14;7:46. doi: 10.1186/1745-6150-7-46.
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.
Wolf YI, Makarova KS, Yutin N, Koonin EV.

ArrayGene 0.3 – Analysis of Genome Centered Microarray Annotation Information

ArrayGene 0.3

:: DESCRIPTION

ArrayGene is a software package for the annotation of microarrays with gene identifiers. The distinctive feature of ArrayGene is the capability of using genomic position of genes to develop comparisons of gene coverage for specific regions of the genome. It provides the tools to construct and maintain custom databases of genes and microarrays probes. It also provides web forms to query the database and create online reports.

::DEVELOPER

Animal Genomics Laboratory ,Department of Animal Science, UC Davis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • MySQL

:: DOWNLOAD

 ArrayGene

:: MORE INFORMATION

Citation

Verdugo, R. A., and J. F. Medrano. 2006.
Comparison of gene coverage of mouse oligonucleotide microarray platforms.
BMC Genomics 2006, 7:58 (doi:10.1186/1471-2164-7-58

RetroMap 0.021 – Characterize LTR Retroelements on a Genome Scale

RetroMap 0.021

:: DESCRIPTION

RetroMap is an application designed to help characterize LTR retroelements on a genome scale in a visually interactive manner. This is NOT a particularly great for comprehensive identification of elements found in highly nested contexts. Only the most internal element of those which are nested is likely to be identified as a complete element. The other elements will be treated as solo LTRs and internal regions depending on how you have set up your element searches. However, it is still a handy way to get a quick visual overview of the situation and create pretty figures.

::DEVELOPER

Brooke D. Peterson-Burch. 

:: SCREENSHOTS

RetroMap

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Java

:: DOWNLOAD

 RetroMap

:: MORE INFORMATION

Citation

Genome Biol. 2004;5(10):R78. Epub 2004 Sep 29.
Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae.
Peterson-Burch BD, Nettleton D, Voytas DF.

PrimerSelect – Computes the AES score for each position in a Genome given a random Primer 5′ tag

PrimerSelect

:: DESCRIPTION

PrimerSelect is a program that computes the AES score for each position in a genome given a random primer 5′ tag.

:: DEVELOPER

Genome Institute of Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 PrimerSelect

:: MORE INFORMATION

Citation

Genome Biol. 2007;8(5):R93.
Optimization and clinical validation of a pathogen detection microarray.
Wong CW, Heng CL, Wan Yee L, Soh SW, Kartasasmita CB, Simoes EA, Hibberd ML, Sung WK, Miller LD.

Breakpoint Calculator 0.2.1 – Calculate Breakpoint Counts for each pair and triplet of Genomes

Breakpoint Calculator 0.2.1

:: DESCRIPTION

Breakpoint Calculator calculates pairwise and three-way hidden breakpoint counts for each pair and triplet of genomes.The breakpoint calculator constructs a weighted graph from the adjacencies of the genomes in the alignment and computes a maximum weight perfect matching.

::DEVELOPER

Birte Kehr., Knut Reinert, and Aaron Darling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

  Breakpoint Calculator

:: MORE INFORMATION

Citation

Birte Kehr, Knut Reinert, Aaron Darling
Hidden breakpoints in genome alignments
WABI 2012

Crossbow 1.2.1 – Whole Genome Resequencing Analysis

Crossbow 1.2.1

:: DESCRIPTION

Crossbow is a scalable, portable, and automatic Cloud Computing tool for finding SNPs from short read data. It combines Bowtie, an ultrafast and memory efficient short read aligner, and SoapSNP, and an accurate genotyper. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. The pipeline can analyze over 35x coverage of a human genome in one day on a 10-node local cluster, or in 3 hours for about $85 using a 40-node, 320-core cluster rented from Amazon Web Services.

Crossbow Online Version

::DEVELOPER

Ben Langmead & Michael Schatz AT the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Crossbow

:: MORE INFORMATION

Citation

Langmead B, Schatz M, Lin J, Pop M, Salzberg SL.Searching for SNPs with cloud computing.Genome Biology 10:R134.

VAAL 46233 – Genome Variant Detection

VAAL 46233

:: DESCRIPTION

VAAL (Variant Ascertainment ALgorithm) is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. On bacterial data sets, it achieves very high sensitivity, and near perfect specificity. VAAL can be used to compare reads from one strain to a reference sequence from another strain. It can also be used to compare reads from two strains to each other, using a third strain to determine homology. For example, we have used VAAL to find a single mutation responsible for bacterial resistance: the output of the program was that single mutation and no others.

::DEVELOPER

Computational R&D, The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

VAAL

:: MORE INFORMATION

Citation

Nusbaum C, Ohsumi TK, Gomez J, Aquadro J, Victor TC, Warren RM, Hung DT, Birren BW, Lander ES, Jaffe DB. Jan 2009.
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
Nature Methods 6: 67–9.

BopGenomes – Compares Genomes in terms of the Presence/Absence of short DNA Segment

BopGenomes

:: DESCRIPTION

The BopGenomes suite is a set of programs that compares genomes in terms of the presence/absence of short DNA segments without requiring genome alignment.

::DEVELOPER

Bellingham Research Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 BopGenomes

:: MORE INFORMATION

Sequence Maneuverer – Sequence Extraction from Genomes

Sequence Maneuverer

:: DESCRIPTION

Sequence Maneuverer is a java based software package having three modules which can be used independently or sequentially. The tool efficiently extracts sequences from large datasets with few simple steps. It can efficiently extract multiple sequences of any desired length from a genome of any organism.

::DEVELOPER

Department of Bio Sciences,COMSATS Institute of Information Technology

:: SCREENSHOTS

SM

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Sequence Maneuverer

:: MORE INFORMATION

Citation

Bioinformation. 2012;8(25):1277-9. doi: 10.6026/97320630081277. Epub 2012 Dec 19.
Sequence Maneuverer: tool for sequence extraction from genomes.
Yasmin T, Rehman IU, Ansari AA, Liaqat K, Khan MI.

Readscan 0.5 – Pathogen Discovery program with accurate genome relative abundance estimation.

Readscan 0.5

:: DESCRIPTION

READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.

:DEVELOPER

Computational Bioscience Research Center ,  King Abdullah University of Science and Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Perl

:: DOWNLOAD

 Readscan

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 1;29(3):391-2. doi: 10.1093/bioinformatics/bts684. Epub 2012 Nov 28.
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation.
Naeem R, Rashid M, Pain A.