ConsensusFixer 0.4 – Consensus Sequence Caller with Ambiguous bases and in-frame Insertions

ConsensusFixer 0.4

:: DESCRIPTION

ConsensusFixer is a java command line application which computes a consensus sequence with in-frame insertions and ambiguous nucleotide (wobbles) from ultra deep next-generation sequencing alignments.

::DEVELOPER

Armin Töpfer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java

:: DOWNLOAD

 ConsensusFixer

:: MORE INFORMATION

TEclass 2.1.3 – Classification of TE Consensus Sequences

TEclass 2.1.3

:: DESCRIPTION

TEclass classifies unknown transpsosable element (TE) consensus sequences into four categories, according to their mechanism of transposition: DNA transposons, LTRs, LINEs, SINEs.

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  TEclass

:: MORE INFORMATION

Citation

Abrusan G., Grundmann N., DeMeester L., Makalowski W. 2009.
TEclass: a tool for automated classification of unknown eukaryotic transposable elements.
Bioinformatics 25:1329-1330

GenomeCons 1.0 – Manipulate Multiple Genome Sequence Alignments and their Consensus Sequences

GenomeCons 1.0

:: DESCRIPTION

GenomeCons is a web server to manipulate multiple genome sequence alignments and their consensus sequences for high-throughput genome sequence analyses.

::DEVELOPER

GenomeCons team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 GenomeCons

:: MORE INFORMATION

Citation

GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences.
Sato T, Suyama M.
Bioinformatics. 2014 Dec 4. pii: btu803.

Refcomp 4.x – Compare Reference Sequence with Consensus Sequence

Refcomp 4.x

:: DESCRIPTION

Refcomp was designed to analyze sequencing traces which contains data from strictly homozygous samples (eg. cloned DNA, mitochondrial DNA, etc.).  This data represents a special case which can be analyzed for mismatches with a known reference sequence.  Refcomp will determine the high quality positions within an assembled DNA contig and produce a report listing sites which differ from a defined reference sequence.

Refcomp is designed as a member of an integrated suite of sequence analysis applications which includes Phred,Phrap and Consed, and is not a stand alone program.

::DEVELOPER

Dr. Deborah Nickerson’s lab at the University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX/Solaris/SGI IRIX/Compaq Tru64 Alpha/HP-UX

:: DOWNLOAD

Refcomp

:: MORE INFORMATION

RefComp is available for free to researchers at academic and non-profit institutions. To aquire RefComp, please Read the Academic License Agreement, and fill in and submit the request form.

Citation:

Rieder et al,Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome., Nucleic Acids Research, 26: 967-973, 1998.