Tag: EST

UIcluster 3.0.5 – Parallel Clustering of EST (Gene) Sequences

UIcluster 3.0.5

:: DESCRIPTION

UIcluster is an updated version of tlcluster that is much faster and adds new features such as reverse complement checking. In addition to optimization and reverse checking, it performs an extended search of all primaries for each sequence being clustered.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

UIcluster

:: REQUIREMENTS

  • Linux / Winodows / MacOsX
  • C Comipiler
  • Java

:: DOWNLOAD

 UIcluster

:: MORE INFORMATION

Citation

K.T. Pedretti,
Accurate, Parallel Clustering of EST (Gene) Sequences,
Masters Thesis, Department of Electrical and Computer Engineering, University of Iowa, May 2001.

UITagCreator 1.9 – Creation of Fixed-length Pooled Library tags for EST-Based Gene Discovery

UITagCreator 1.9

:: DESCRIPTION

UITagCreator is used for the creation of fixed-length pooled library tags for EST-Based Gene Discovery.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Comipiler

:: DOWNLOAD

  UITagCreator

:: MORE INFORMATION

ESTate 0.5 – Expressed Sequence Tag Analysis Tools Etc

ESTate 0.5

:: DESCRIPTION

ESTate (Expressed Sequence Tag Analysis Tools Etc) is a package for EST analysis.

::DEVELOPER

Guy Slater (gslater@hgmp.mrc.ac.uk)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Mac OsX/ Linux
  • C Complier

:: DOWNLOAD

  ESTate

:: MORE INFORMATION

EST-PAC – A simple EST management tool and Annotation Pipeline

EST-PAC

:: DESCRIPTION

EST-PAC is a web based tool for the annotation of bio-sequences.

::DEVELOPER

Yvan Strahm

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • PHP
  • MySQL
  • Apache

:: DOWNLOAD

  EST-PAC

:: MORE INFORMATION

Citation

Yvan Strahm, David Powell and Christophe Lefevre.
EST-PAC a web package for EST annotation and protein sequence prediction.
Source Code Biol Med. 2006 Oct 12;1:2

ESTminer 1.0 – Mining EST Contig and Cluster databases

ESTminer 1.0

:: DESCRIPTION

ESTminer is a Web application and database schema for interactive mining of expressed sequence tag (EST) contig and cluster data sets.  The Web interface contains a query frame that allows the selection of contigs/clusters with specific cDNA library makeup or threshold number of members with the results displayed as color-coded tree nodes where the color indicats the fractional size of each cDNA library component.  The nodes are expandable, revealing library statistics as well as EST or contig members with links that can be configured for sequence data, GenBank records, or other user configurable links.  Also, the interface allows “queries within queries” where the result set of a query is further filtered by the subsequent query.

::DEVELOPER

ESTminer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JAKARTA TOMCAT
  • MySQL

:: DOWNLOAD

  ESTminer

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Mar 1;21(5):669-70.
ESTminer: a Web interface for mining EST contig and cluster databases.
Huang Y, Pumphrey J, Gingle AR.

AFST 1.0 – Abnormality Filtering and Sequence Trimming for ESTs

AFST 1.0

:: DESCRIPTION

 AFST(Abnormality Filtering and Sequence Trimming for ESTs)is a software tool using a pattern analysis approach.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 AFST 

:: MORE INFORMATION

Citation:

Sun Zhou, Guoli Ji, Xiaolin Liu, Li P++, Moler J, Karro JE and Liang C (2012)
Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data.
BMC Biotechnology, 12:16. doi:10.1186/1472-6750-12-16

Expeditor 2 – Design Primers using Human Gene Structure and EST information of your Species

Expeditor 2

:: DESCRIPTION

Expeditor is a tool for designing gene-specific primers targeted at genomic regions of interests based on known gene structure and EST sequence information

::DEVELOPER

NAGRP Bioinformatics Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

J Hered. 2005 Jan-Feb;96(1):80-2. Epub 2004 Dec 14.
Expeditor: a pipeline for designing primers using human gene structure and livestock animal EST information.
Hu ZL, Glenn K, Ramos AM, Otieno CJ, Reecy JM, Rothschild MF.

JANE – EST Analyzer

JANE

:: DESCRIPTION

JANE (Just Analyze Nucleotides and ESTs) provides a feasible plan for rapid analysis of EST sequences using a related genome as template to align all the ESTs. The homology modeling results in a virtual genome, with annotation for systematical analysis.

::DEVELOPER

JANE Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Nov 29;10:391.
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
Liang C, Schmid A, López-Sánchez MJ, Moya A, Gross R, Bernhardt J, Dandekar T.