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.

Jstacs 2.2 – Java Framework for Statistical Analysis and Classification of Biological Sequences

Jstacs 2.2

:: DESCRIPTION

Jstacs is an open source Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches for parameter learning. Using Jstacs, classifiers can be assessed and compared on test datasets or by cross-validation experiments evaluating several performance measures.

::DEVELOPER

Jstacs Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 Jstacs

:: MORE INFORMATION

Citation

Michael Seifert, Marc Strickert, Alexander Schliep and Ivo Grosse
Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models
Bioinformatics (2011) 27 (12): 1645-1652.

BATS – A Basic Analysis Toolkit for Biological Sequences

BATS

:: DESCRIPTION

BATS consists of a collection of libraries that can be used to run basic sequence analysis tasks. Routines for global alignment (LCS from Fragments, Edit Distance with Gaps), local alignment (approximata string matching with K mismateches or differences), and statistical analysis (Filter, Z-Score and Model Generation ) are included.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

BATS2

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Perl

:: DOWNLOAD

 BATS

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2007 Sep 18;2:10.
A basic analysis toolkit for biological sequences.
Giancarlo R1, Siragusa A, Siragusa E, Utro F.

Kolmogorov – Compression-based Classification of Biological Sequences and Structures

Kolmogorov

:: DESCRIPTION

Kolmogorov is a multistep approach to classify and cluster Biological Sequences and Structures, via Compression.

::DEVELOPER

Raffaele Giancarlo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • Perl
  • BioPerl

:: DOWNLOAD

 Kolmogorov

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 13;8:252.
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
Ferragina P1, Giancarlo R, Greco V, Manzini G, Valiente G.

Seqinr 3.1-3 – Biological Sequences Retrieval and Analysis in R

Seqinr 3.1-3

:: DESCRIPTION

The seqinR package for the R environment is a library of utilities to retrieve and analyse biological sequences.

::DEVELOPER

Leonor Palmeira.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Seqinr

:: MORE INFORMATION

D. Charif, J. Thioulouse, J. R. Lobry and G. Perrière
Online synonymous codon usage analyses with the ade4 and seqinR packages
Bioinformatics (2005) 21 (4): 545-547

BioSAVE 0.11 – Biological Sequence Annotation Viewer

BioSAVE 0.11

:: DESCRIPTION

BioSAVE is a program for visualising DNA or protein sequences and annotations thereof. Annotations is used in a very broad sense here, encompassing any annotation that may be expressed in GFF format.

::DEVELOPER

Richard Pollock and Boris Adryan

:: SCREENSHOTS

BioSAVE

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 BioSAVE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Mar 20;9:157. doi: 10.1186/1471-2105-9-157.
BioSAVE: display of scored annotation within a sequence context.
Pollock RF1, Adryan B.