Sequin 15.10 – Submit & Update Entries to the GenBank Sequence Database

Sequin 15.10

:: DESCRIPTION

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank,  EMBL, and DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, gapped sequences, or phylogenetic and population studies.

::DEVELOPER

the National Center for Biotechnology Information

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Sequin

:: MORE INFORMATION

Pozitiv 1.1 – Sequence Database Mining and Alignment program

Pozitiv 1.1

:: DESCRIPTION

POZITIV is a collection of Python modules which implements various sequencing algorithms such as Smith-Waterman and the Pozitiv variant itself.

::DEVELOPER

The Centre for Bioinformation Science (CBiS)at The Australian National University (ANU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Pozitiv

:: MORE INFORMATION

Citation:

Normalisation of Sequence Alignment Scores
Hilary S. Booth, John H. Maindonald, Ole M. Nielsen, Susan R. Wilson
January 2003.

ARB 6.0.3 – Sequence Database Handling and data analysis

ARB 6.0.3

:: DESCRIPTION

The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.

::DEVELOPER

Lehrstuhl für Mikrobiologie, TU München

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ARB

:: MORE INFORMATION

Citation:

Wolfgang Ludwig, et al.
ARB: a software environment for sequence data.
Nucleic Acids Research. 2004. 32(4):1363-1371.

Targetfinder 1.7 – Predict Small RNA Targets in a Sequence Database

Targetfinder 1.7

:: DESCRIPTION

Targetfinder predicts small RNA targets in a sequence database using a plant-based scoring metric.

::DEVELOPER

the Carrington Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 Targetfinder

:: MORE INFORMATION

Citation:

Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. (2007)
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.
PLoS ONE 2, e219.

ThermonucleotideBLAST 2.01 – Searching Nucleic Acid-based Assays against Sequence Databases

ThermonucleotideBLAST 2.01

:: DESCRIPTION

ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query.

::DEVELOPER

Jason D. Gans

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

  ThermonucleotideBLAST

:: MORE INFORMATION

Oligomap 1.01 – Identification of nearly-perfect matches of small RNAs in Sequence databases

Oligomap 1.01

:: DESCRIPTION

Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases. It allows to exhaustively identify all the perfect and 1-error (where an error is defined to be a mismatch, insertion or deletion) matches of large sets of small RNAs to target sequences. Optimal performance is achieved at about 500000 query sequences

::DEVELOPER

Zavolan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Oligomap

:: MORE INFORMATION

Citation

Berninger P, Gaidatzis D, van Nimwegen E, Zavolan M.
Computational analysis of small RNA cloning data“,
Methods, 44(13-21), 2008