EGassembler – Automatic Generation of Consensus Contigs from a set of ESTs

EGassembler

:: DESCRIPTION

EGassembler is a web server, which provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling of ESTs and genomic fragments.

::DEVELOPER

Kyoto University Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W459-62.
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.
Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S.

FindTail 1.01 – Accurate Detection of Poly(A)/(T) tails and other Homopolymer in RNA-Seq and ESTs

FindTail 1.01

:: DESCRIPTION

Implemented in C++, FindTail first detects all perfect poly(A) tracts (or homopolymers)in a sequence. Starting with the first tract, FindTail then determines whether the downstream tracts can be merged to form a longer poly(A) fragment using an adjustable gap. After the merging step, it calculates the identity for all resultant poly(A) fragments and remaining tracts, and filter them using an adjustable minimum identity. Finally, the poly(A) length is calculated and filtered by an adjustable minimum length.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • C++ Compiler

:: DOWNLOAD

 FindTail

:: MORE INFORMATION

SeqClean 20110222 – Trim & Validation of ESTs or other DNA sequences

SeqClean 20110222

:: DESCRIPTION

SeqClean (Sequence Cleaner) is a script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences.

::DEVELOPER

The Gene Index Project

:: REQUIREMENTS

:: DOWNLOAD

 SeqClean

:: MORE INFORMATION

Citation:

An optimized procedure greatly improves EST vector contamination removal.
Chen YA, Lin CC, Wang CD, Wu HB, Hwang PI.
BMC Genomics. 2007 Nov 13;8:416.