Tag: Sequence

SDT v1.2 – Sequence Demarcation Tool

SDT v1.2

:: DESCRIPTION

SDT is a free and easy to use program that allows classification of virus sequences based on sequence pairwise identity. It takes as input a FASTA file of aligned or unaligned DNA or protein sequences and aligns every unique pair of sequences, calculates pairwise similarity scores, and displays a colour coded matrix of these scores. It also produces both a plot of these pairwise identity scores and text files containing analysis results.

::DEVELOPER

the University of Cape Town (UCT) Computational Biology (CBIO) Group 

:: SCREENSHOTS

SDTv

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 SDT

:: MORE INFORMATION

Citation:

PLoS One. 2014 Sep 26;9(9):e108277. doi: 10.1371/journal.pone.0108277. eCollection 2014.
SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.
Muhire BM1, Varsani A2, Martin DP

DynaMine Beta – Predicting Protein Dynamics from Sequence

DynaMine Beta

:: DESCRIPTION

DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input.

::DEVELOPER

DynaMine team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DynaMine

:: MORE INFORMATION

Citation

The DynaMine webserver: predicting protein dynamics from sequence.
Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W264-70. doi: 10.1093/nar/gku270

PEASE – Predicting Epitopes using Antibody Sequence

PEASE

:: DESCRIPTION

PEASE is an automated tool for predicting the epitope for a given antigen structure and an antibody sequence.

::DEVELOPER

Yanay Ofran’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PEASE: Predicting B-Cell Epitopes utilizing Antibody Sequence.
Sela-Culang I, Ashkenazi S, Peters B, Ofran Y.
Bioinformatics. 2014 Nov 27. pii: btu790

PCSS – Peptide Classification using Sequence and Structure

PCSS

:: DESCRIPTION

PCSS is a web server that allows a user to train new SVM models to make predictions for any protein that recognizes specific oligopeptide ligands.

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1714-22. doi: 10.1093/bioinformatics/btq267. Epub 2010 May 26.
Prediction of protease substrates using sequence and structure features.
Barkan DT1, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A.

AlphaMALIG 1.1 – Aligns Sequences in a given Alphabet

AlphaMALIG 1.1

:: DESCRIPTION

AlphaMALIG  (ALPHAbet Multiple ALIGnment) is a tool which allows you to align many but no more than 200 sequences. These sequences will be formed by characters of a finite alphabet.

::DEVELOPER

 the Algorithmics and Genetics Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C compiler

:: DOWNLOAD

  AlphaMALIG

:: MORE INFORMATION

TableParser – Extract Sequences from Tab-delimited Assembly Alignment Files

TableParser

:: DESCRIPTION

TableParser: Simple tool for extracting sequences from tab-delimited assembly alignment files (e.g. SimAssembly and AceParser output). Parses out contigs, singletons, and assembled reads into separate files.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 TableParser

:: MORE INFORMATION

SEQPower 1.1.0 – Power Analysis for Sequence-based Association Studies

SEQPower 1.1.0

:: DESCRIPTION

SEQPower provides statistical power analysis and sample size estimation for sequence-based association studies

::DEVELOPER

SEQPower team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  SEQPower

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 28. pii: btu296. [Epub ahead of print]
Power analysis and sample size estimation for sequence-based association studies.
Wang GT, Li B, Lyn Santos-Cortez RP, Peng B, Leal SM.

CLOSET r78 – CLoud Open SequencE clusTering

CLOSET r78

:: DESCRIPTION

CLOSET is a map-reduce framework for clustering sequences from metagenomic samples, such as 454 reads.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • HADOOP cluster

:: DOWNLOAD

  CLOSET

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340001. doi: 10.1142/S0219720013400015. Epub 2012 Dec 25.
Large-scale metagenomic sequence clustering on map-reduce clusters.
Yang X1, Zola J, Aluru S.

Triplet-SVM – Predict a query sequence with Hairpin Structure as a real miRNA precursor or not

Triplet-SVM

:: DESCRIPTION

Triplet-SVM is developed for predicting a query sequence with hairpin structure as a real miRNA precursor or not. The triplet-SVM classifier analyzes the triplet elements of the query and predicts it using a SVM classifier. The SVM classifier is previously trained based on the triplet element features of a set of real miRNA precursors and a set of pseudo-miRNA hairpins.

::DEVELOPER

Triplet-SVM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Triplet-SVM

:: MORE INFORMATION

Citation

Chenghai Xue, Fei Li, Tao He, Guoping Liu, Yanda Li, Xuegong Zhang,
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine,
BMC Bioinformatics, 6: 310, 2005