Tag: Biological Sequence

motif-x 1.2 – Biological Sequence Motif Discovery

motif-x 1.2

:: DESCRIPTION

motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.

::DEVELOPER

Schwartz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2011 Sep;Chapter 13:Unit 13.15-24. doi: 10.1002/0471250953.bi1315s35.
Biological sequence motif discovery using motif-x.
Chou MF, Schwartz D.

KeBABS 1.20.0 – R Package for Kernel-Based Analysis of Biological Sequences

KeBABS 1.20.0

:: DESCRIPTION

The KeBABS package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define similarity measures between sequences.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  KeBABS

:: MORE INFORMATION

Citation

KeBABS: an R package for kernel-based analysis of biological sequences.
Palme J, Hochreiter S, Bodenhofer U.
Bioinformatics. 2015 Mar 25. pii: btv176.

ALN 3.5.2 – Pairwise Alignment of Biological Sequences Supporting Spliced Alignment Procedures

ALN 3.5.2

:: DESCRIPTION

Aln is a program for aligning a pair of nucleotide or amino acid sequences or groups of sequences. Aln accepts various combinations of distinct types of inputs: a single nucleotide sequence (SN), a single amino acid sequence (SA), a pre-aligned group of nucleotide sequences (MN), and a group of amino acid sequences (MA). Notably, aln can now perform mixed alignment between a nucleotide sequence and a protein sequence or a group of protein sequences [5]. This novel feature of aln enables us to predict eukaryotic gene structures (protein-coding exons) based on sequence homology with known protein sequence(s). The details of this procedure will be described in a later section entitled ‘Gene-structure prediction’.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 ALN

:: MORE INFORMATION

Citation

Gotoh, O. (2000)
” Homology-based gene structure prediction: simplified matching algorithm by the use of translated codon (tron) and improved accuracy by allowing for long gaps.”
Bioinformatics, 16, 190-202.

Protael 1.1.0 – JavaScript Library for Visualizing Biological Sequences and related data

Protael 1.1.0

:: DESCRIPTION

Protael is a vector graphics library for displaying various biological sequence related data on web pages.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript
:: DOWNLOAD

 Protael

:: MORE INFORMATION

Citation:

Protael: protein data visualization library for the web.
Sedova M, Jaroszewski L, Godzik A.
Bioinformatics. 2015 Oct 29. pii: btv605.

IBS 1.0.3 – Illustrator of Biological Sequences

IBS 1.0.3

:: DESCRIPTION

IBS is a software package that can be used for representing the organization of either protein or nucleotide sequences, in a convenient, efficient and precise manner.

::DEVELOPER

Lab of Cell Dynamics, and Lab of Nanobiology,University of Science & Technology of China

:: SCREENSHOTS

IBS

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Java

:: DOWNLOAD

 IBS

:: MORE INFORMATION

Citation

IBS: an illustrator for the presentation and visualization of biological sequences.
Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, Lahrmann U, Zhao Q, Zheng Y, Zhao Y, Xue Y, Ren J.
Bioinformatics. 2015 Jun 10. pii: btv362.

Myblast 1.0.29 – Customized Biological Sequence Alignment tool

Myblast 1.0.29

:: DESCRIPTION

Myblast is the web-application of the customized biological sequence alignment tool.

::DEVELOPER

Lab of Systems and Network Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Myblast

:: MORE INFORMATION