AlignExIn 20130624 – Alignment Exon Intron Structure

AlignExIn 20130624

:: DESCRIPTION

AlignExIn ( Align Exon Intron) is a handy and useful utility built in order to display the alignment of exons. The program displays the exon painted in red and the alignments painted in blue by default, but it is possible to change the colors.All you have to do is select the input files (fasta and exon) and the program will do the rest.

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 alignexin

:: MORE INFORMATION

DeepAlign 1.35 – Pairwise Protein Structure Alignment

DeepAlign 1.35

:: DESCRIPTION

Different from many other tools, DeepAlign aligns two protein structures using evolutionary information and beta strand orientation in addition to geometric similarity. Therefore, DeepAlign favors the alignment of evolutionarily-related residues and also aligns beta sheets more correctly than the others. The DeepAlign alignments are also much more consistent with manual alignments than the others.

::DEVELOPER

Xu group , Sheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DeepAlign

:: MORE INFORMATION

Citation:

Sci Rep. 2013;3:1448. doi: 10.1038/srep01448.
Protein structure alignment beyond spatial proximity.
Wang S, Ma J, Peng J, Xu J.

ASpipe 2.1.8 – Process GeneSeqer/GMAP Alignments & Identify Alternative Splicing

ASpipe 2.1.8

:: DESCRIPTION

ASpipe (alternative splicing) is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments.ASpipe extracts coordinates and scores for high-quality intron/exon/alignments from the original program outputs and stores them in MySQL5.0 databases.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

:: DOWNLOAD

ASpipe

:: MORE INFORMATION

Citation

Wang, B.-B., O’Toole, M., Brendel, V. & Young, N.D. (2008)
Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.
BMC Plant Biol. 8:17.

SAPS/SSPA 20110801 – Statistical Analysis of Protein Sequences & Significant Segment Pair Alignment

SAPS/SSPA 20110801

:: DESCRIPTION

SAPS (statistical analysis of protein sequences) calculates all the statistics for any individual protein sequence input.

SSPA is an acronym for Significant Segment Pair Alignment.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SAPS/SSPA

:: MORE INFORMATION

Citation

SAPS
Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E. & Karlin, S. (1992)
Methods and algorithms for statistical analysis of protein sequences.
Proc. Natl. Acad. Sci. USA 89, 2002-2006.

SSPA
Karlin, S., Weinstock, G. & Brendel, V. (1995)
Bacterial classifications derived from RecA protein sequence comparisons.
J. Bacteriol. 177, 6881-6893.

secureBlast 1.03 – Controlled access to wwwBLAST

secureBlast 1.03

:: DESCRIPTION

secureBLAST supplements NCBI wwwblast with features necessary to control in an easy manageable way usage of BLAST data sets and their update. The concept we implemented allows to offer on a single BLAST server several data sets with individually configurable access rights.

::DEVELOPER

Göttingen Genomics Laboratory, Institut für Mikrobiologie and Genetik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • PHP

:: DOWNLOAD

  secureBlast

:: MORE INFORMATION

Citation

In Silico Biol. 2003;3(4):405-9.
secureBLAST.
Wiezer A, Merkl R.

ProtDeform 1.0 – Protein Structural Alignment

ProtDeform 1.0

:: DESCRIPTION

ProtDeform is a protein structural alignment. It automatically finds the alignments that expert hands define as most likely, and to recognize domains with the same CATH homology and topology.

::DEVELOPER

Computational Biology and Bioinformatics Research Group , University of the Balearic Islands

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 ProtDeform

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jul 1;25(13):1625-31. doi: 10.1093/bioinformatics/btp296.
Flexible structural protein alignment by a sequence of local transformations.
Rocha J, Segura J, Wilson RC, Dasgupta S.

MPAlign-editor 3.0.0 – Graphical Tool for DNA and Protein Sequences and Alignments

MPAlign-editor 3.0.0

:: DESCRIPTION

MPAlign-editor is a graphical tool for DNA and Protein sequences and alignments.

::DEVELOPER

Frederico Arnoldi (fgcarnoldi@gmail.com)

:: SCREENSHOTS

mpalign-editor

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 MPAlign-editor

:: MORE INFORMATION

Citation

MPAlign editor: uma ferramenta gráfica e intuitiva para alinhamentos moleculares.
Frederico GC Arnoldi 2005
Proceedings of II Workshop TIDIA—FAPESP

TreeRefiner 1.1 – Refining Multiple Sequence Alignments

TreeRefiner 1.1

:: DESCRIPTION

TREEREEFINER is an efficient program for refining multiple alignment of genomic sequences based on a phylogenetic tree. It has demonstrated significant improvements in the accuracy of alignments generated by several popular aligners

::DEVELOPER

TreeRefiner  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TreeRefiner

:: MORE INFORMATION

Citation

Proc IEEE Comput Syst Bioinform Conf. 2005:111-9.
TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.
Manohar A, Batzoglou S.

SOCS 2.2 – SOLiD Read Mapper with Bisulfite Sequencing Support

SOCS 2.2

:: DESCRIPTION

SOCS (short oligonucleotide color space) is a SOLiD read mapper with bisulfite sequencing support.SOCS performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. Modes are available for detecting short sequence-space variants (such as SNPs) and for detecting unlimited numbers of bisulfite-induced nucleotide substitutions for 5mC methylation studies.

::DEVELOPER

Nicholas H. Bergman (nickbergman@gatech.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SOCS

:: MORE INFORMATION

Citation

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.
Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH.
Bioinformatics. 2010 Aug 1;26(15):1901-2. doi: 10.1093/bioinformatics/btq291.