Tag: Sequence Analysis

mtDNAprofiler – Mitochondrial DNA Sequence Analysis Tool

mtDNAprofiler

:: DESCRIPTION

mtDNAprofiler is a web program which enables users to analyze and compare mtDNA sequences whether they are indicated as FASTA format or as a difference to revised Cambridge Reference Sequence (rCRS).

::DEVELOPER

Yonsei DNA Profiling Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Forensic Sci. 2013 Jul;58(4):972-80. doi: 10.1111/1556-4029.12139. Epub 2013 May 17.
mtDNAprofiler: a Web application for the nomenclature and comparison of human mitochondrial DNA sequences.
Yang IS1, Lee HY, Yang WI, Shin KJ.

Jnomics 0.2 – Cloud-Scale Sequence Analysis

Jnomics 0.2

:: DESCRIPTION

Jnomics is a cloud-scale sequence analysis suite designed to help meet the computational challenges presented by the continuing revolution in massively parallel DNA sequencing technologies.

::DEVELOPER

Matt Titmus , Schatz Lab, Cold Spring Harbor Laboratory

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • java
  • ANT
  • Apache Hadoop 

:: DOWNLOAD

 Jnomics

:: MORE INFORMATION

Citation

Jnomics-A cloud-scale sequence analysis suite.
Matt Titmus, Sneh Lata, Eric Antonious, James Gurtowski, W. Richard McCombie, and Michael Schatz
Genome Informatics, Cold Spring Harbor NY, Nov 3, 2011.

seqtools 8.4.071 – Program Suite for Sequence Analysis

seqtools 8.4.071

:: DESCRIPTION

Seqtools is a large collection of tools for basic and advanced analyses of nucleotide and protein sequences. The tools are wrapped into a common user interface making handling, storage, retrieval and viewing the results easy and logical. A seqtools project can accommodate many thousand sequences making unattended batch  analyses like database searching at NCBI painless with the robust search engine included in seqtools.

::DEVELOPER

S.W.Rasmussen

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 seqtools

:: MORE INFORMATION

SeqCalc 1.0 – Portable software for Sequence Analysis

SeqCalc 1.0

:: DESCRIPTION

SeqCalc assists the research personnel in computational sequence analysis and automated experimental calculations.

::DEVELOPER

Dhandapani Vignesh, Molecular Genetics and Genomics Lab, Chungnam National University

:: SCREENSHOTS

SeqCalc

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SeqCalc

:: MORE INFORMATION

Citation:

Dhandapani Vignesh, Paul Parameswari, Kim Hae Jin, Lim Yong Pyo. (2010)
SeqCalc: A portable bioinformatics software for sequence analysis.
Bioinformation 5(3): 85-88.

EGene 1.0 – Automated Pipeline Generation System for Sequence Analysis

EGene 1.0

:: DESCRIPTION

EGene is a generic, flexible and modular pipeline generation system that makes pipeline construction a modular job. EGene allows for third-party programs to be used and integrated according to the needs of distinct projects and without any previous programming or formal language experience being required.

Coed is a visual tool to facilitate pipeline construction and documentation.

::DEVELOPER

EGene Team

:: SCREENSHOTS

EGene

:: REQUIREMENTS

  • Linux
  • Java
  • Perl
  • PostgreSQL

:: DOWNLOAD

  EGene , Coed

:: MORE INFORMATION

Citation:

Durham, A.M.; Kashiwabara, A.Y.; Matsunaga, F.T.; Ahagon, P.H.; Rainone, F.; Varuzza, L. & Gruber A. (2005).
EGene: a configurable pipeline generation system for automated sequence analysis. 
Bioinformatics 21(12): 2812-2813.

SBSPKS – Structure Based Sequence Analysis of Polyketide Synthases

SBSPKS

:: DESCRIPTION

SBSPKS is a webserver for carrying out sequence and structure based analysis of Polyketide Synthases, an important family of multifunctional megasynthases involved in the biosynthesis of a variety of pharmaceutically important secondary metabolites. The knowledge base for development of SBSPKS is derived from a comprehensive bioinformatics analysis of the sequence and structural features of a large number of experimentally characterized PKS gene clusters having known metabolic products and recently available crystal structures of PKS and FAS proteins.The interfaces for carrying out various tasks by SBSPKS are organized as three major functional units, namely NRPS_PKS, Model_3D_PKS and Dock_Dom_Anal .

::DEVELOPER

Debasisa Mohanty

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W487-96. Epub 2010 May 5.
SBSPKS: structure based sequence analysis of polyketide synthases.
Anand S, Prasad MV, Yadav G, Kumar N, Shehara J, Ansari MZ, Mohanty D.

RNASEQR 1.0.2 – Streamlined and Accurate RNA-seq Sequence Analysis program

RNASEQR 1.0.2

:: DESCRIPTION

RNASEQR is a nucleotide sequence mapper/aligner and is designed specifically for RNA-seq data analysis. It takes advantage of annotated transcripts and genomic reference sequences to obtain high quality mapping/alignment results.

::DEVELOPER

Hood Lab at ISB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  RNASEQR

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Mar;40(6):e42. Epub 2011 Dec 22.
RNASEQR–a streamlined and accurate RNA-seq sequence analysis program.
Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.

MUNGO 1.0 – Python Library of Sequence Analysis

MUNGO 1.0

:: DESCRIPTION

MUNGO is a python library supporting parsing, manipulation and visualisation of sequence analysis results

::DEVELOPER

Dr Tony Papenfuss (papenfuss@wehi.edu.au) @ WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 MUNGO

:: MORE INFORMATION

EMOTIF 3.6 – Sequence Analysis Using Pareto-optimal Discrete Motifs

EMOTIF 3.6

:: DESCRIPTION

EMOTIF includes the following three programs:

(1) eMOTIF-SEARCH: Given a protein sequence, the eMOTIF-SEARCH program suggests families of proteins to which the query sequence may belong. The eMOTIF-SEARCH program considers a protein sequence a potential member of a protein family, if the sequence contains discrete motif or motifs that have been generated from an ungapped multiple sequence alignment of known member sequences from that family.

(2) eMOTIF-MAKER: The eMOTIF-MAKER program converts an ungapped multiple sequence alignment into a set of Pareto-optimal discrete motifs for use by the eMOTIF-SEARCH program and the eMOTIF-SCAN program. The resulting set of motifs often reveals sub-families within the cluster of proteins that share the region of sequence similarity covered by the given ungapped multiple sequence alignment.

(3) eMOTIF-SCAN: Given a regular expression, the eMOTIF-SCAN program finds all the occurrences of that regular expression in a particular sequence database.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • C Complier

:: DOWNLOAD

  EMOTIF

:: MORE INFORMATION

Citation:

Nevill-Manning, C. G., Wu, T. D. and Brutlag, D. L. (1998).
Highly Specific Protein Sequence Motifs for Genome Analysis.
Proc. Natl. Acad. Sci. May 26, 1998 vol. 95 no. 11 5865-5871