Tag: Microbial Genome

GOST 0.1 – Detect Orthologous Relationship in Microbial Genomes

GOST 0.1

:: DESCRIPTION

GOST (Globally Optimized Strategy ) is a program to detect orthologous relationship in microbial genomes.

::DEVELOPER

Qin Ma  , Bioinformatic and Mathematical Biosciences Lab, The Ohio State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GOST 

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Dec;39(22):e150. Epub 2011 Sep 29.
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.
Li G, Ma Q, Mao X, Yin Y, Zhu X, Xu Y.

dRep 3.2.2 – De-replication of Microbial Genomes

dRep 3.2.2

:: DESCRIPTION

dRep is a python program for rapidly comparing large numbers of genomes. dRep can also “de-replicate” a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/windows /MacOsX
  • Python

:: DOWNLOAD

dRep

:: MORE INFORMATION

Citation

Olm MR, Brown CT, Brooks B, Banfield JF.
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.
ISME J. 2017 Dec;11(12):2864-2868. doi: 10.1038/ismej.2017.126. Epub 2017 Jul 25. PMID: 28742071; PMCID: PMC5702732.

PhiSpy 3.7.8 – Find Prophages in Microbial Genomes

PhiSpy 3.7.8

:: DESCRIPTION

PhiSpy is a novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PhiSpy

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep;40(16):e126. doi: 10.1093/nar/gks406. Epub 2012 May 14.
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies.
Akhter S1, Aziz RK, Edwards RA.

PPFS 2 – Add on to kSNP for predicting Phenotypes from SNPs in Microbial Genome

PPFS 2

:: DESCRIPTION

The PPFS (Predict Phenotypes From SNPs) package is an add-on to kSNP , a program that can identify SNPs in a data set of hundreds of microbial genomes.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

PPFS

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 28;9(2):e90490. doi: 10.1371/journal.pone.0090490. eCollection 2014.
SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments.
Hall BG1.

FindPlasmids 20180522 – Find plasmids in Microbial Genome Assembly Files

FindPlasmids 20180522

:: DESCRIPTION

FindPlasmids identifies known plasmids in genome assembly files by using the assembly file to query a local Blast+ database of plasmid sequences.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

FindPlasmids

:: MORE INFORMATION

 

GWFASTA – FASTA search in Eukaryotic and Microbial Genomes

GWFASTA

:: DESCRIPTION

GWFASTA (Genome Wise Sequence Similarity Search using FASTA) allows user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search

::DEVELOPER

GWFASTA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Issac, B. and Raghava, G. P. S.(2002)
GWFASTA: A server for FASTA search in Eukaryotic and Microbial genomes.
BioTechniques 33(3):548-556.

TriTISA – Prediction of Translation Initiation Site for Microbial Genomes

TriTISA

:: DESCRIPTION

TriTISA is a Bayesian methodology based method for translation initiation site (TIS) prediction in microbial genomes.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  TriTISA

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jan 1;25(1):123-5. doi: 10.1093/bioinformatics/btn576. Epub 2008 Nov 10.
Prediction of translation initiation site for microbial genomes with TriTISA.
Hu GQ1, Zheng X, Zhu HQ, She ZS.

BugBuilder – Microbial Genome Assembly

BugBuilder

:: DESCRIPTION

BugBuilder is a pipeline for the automated assembly and annotation of microbial genomes from high-throughput sequence data. It is configurable so as not to be tied to any assembler or scaffolder, and is designed to run in a cluster environment facilitating high-throughput processing of genomes.

::DEVELOPER

James Abbott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 BugBuilder

:: MORE INFORMATION

OperonDB 2.1 – Database of Predicted operons in Microbial Genomes

OperonDB 2.1

:: DESCRIPTION

OperonDB is a database containing the results of a computational algorithm for locating operon structures in microbial genomes. OperonDB has grown from 34 genomes in its initial release to more than 500 genomes today. In addition to increasing the size of the database, we have re-designed our operon finding algorithm and improved its accuracy.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OperonDB

:: MORE INFORMATION

Citation:

M. Pertea et al.,
OperonDB: a comprehensive database of predicted operons in microbial genomes
Nucl. Acids Res 37 (2009), D479-D482.

AGMIAL – Annotate Microbial Genomes

AGMIAL

:: DESCRIPTION

AGMIAL is an integrated system for bacterial genome annotation. It is currently used at INRA for the newly sequenced bacterial genomes : Lactobacillus bulgaricus, Lactobacillus sakei and Flavobacterium psychrophilum, as well as the re-annotation of Lactococcus lactis, Enterococcus faecalis and faecium.

::DEVELOPER

AGMIAL Team at Jouy-en-Josas Cedex

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

AGMIAL Source Code

:: MORE INFORMATION

Citation:

K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin JF. Gibrat.
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.
Nucleic Acids Research. Jul 2006.