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

SLPFA – Subcellular Location Prediction with Frequency and Alignment

SLPFA

:: DESCRIPTION

SLPFA is a predictor for subcellular location prediction of proteins by feature vectors based on amino acid composition (frequency) and sequence alignment. 90.96% of overall accuracy was obtained through fivefold cross validation tests with TargetP plant data sets.

SLPFA is an improved subcellular location predictor of SLP-Local

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Nov 30;8:466.
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
Tamura T, Akutsu T.

ProteinEvolverABC – Estimation of Recombination and Substitution Rates in Alignments of Protein Sequences

ProteinEvolverABC

:: DESCRIPTION

The package ProteinEvolverABC is a computer framework to estimate recombination and substitution rates in multiple alignments of protein sequences by approximate Bayesian computation.

::DEVELOPER

CME Group

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

ProteinEvolverABC

:: MORE INFORMATION

Citation

Arenas M.
ProteinEvolverABC: Coestimation of Recombination and Substitution Rates in Protein Sequences by approximate Bayesian computation.
Bioinformatics. 2021 Aug 27:btab617. doi: 10.1093/bioinformatics/btab617. Epub ahead of print. PMID: 34450622.

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.

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

NOFOLD 1.0.1 – RNA Structure Clustering without Folding or Alignment

NOFOLD 1.0.1

:: DESCRIPTION

NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment. It works by mapping each RNA sequence of interest to a structural feature space, where each coordinate within the space corresponds to the probabilistic similarity of the sequence to an empirically defined structure model (e.g. Rfam family covariance models).

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

NOFOLD

:: MORE INFORMATION

Citation

Middleton SA, Kim J.
NoFold: RNA structure clustering without folding or alignment.
RNA. 2014 Nov;20(11):1671-83. doi: 10.1261/rna.041913.113. Epub 2014 Sep 18. PMID: 25234928; PMCID: PMC4201820.

GCAligner 1.0 – Alignment of Chemical data obtained by Gas Chromatography

GCAligner 1.0

:: DESCRIPTION

GCAligner  is a software designed to perform a preliminary alignment of chemical data obtained by gas chromatography. It was created to facilitate the comparison of multiple samples. The alignment algorithm is based on the comparison between each retention time, the following retention time in the same sample and its closest retention times in other samples. GCAligner is a java executable software running on any operating system. The input data file and the single output file containing the align data set are text files with tab delimited pieces of information.
See the software manual for further details.

::DEVELOPER

Simon Dellicour and Thomas Lecocq @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

   GCAligner

:: MORE INFORMATION

TwinCons – Alignment Score for detection of Ancient Homologies

TwinCons

:: DESCRIPTION

TwinCons is a software to detect noisy signals of deep ancestry of proteins or nucleic acids.

::DEVELOPER

The Williams Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TwinCons

:: MORE INFORMATION

Citation

Penev PI, Alvarez-Carreño C, Smith E, Petrov AS, Williams LD.
TwinCons: Conservation score for uncovering deep sequence similarity and divergence.
PLoS Comput Biol. 2021 Oct 29;17(10):e1009541. doi: 10.1371/journal.pcbi.1009541. PMID: 34714829; PMCID: PMC8580257.

Minimap2 v2.23 – Pairwise Alignment for Nucleotide Sequences

Minimap2 v2.23

:: DESCRIPTION

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Minimap2

:: MORE INFORMATION

Citation

Li H.
New strategies to improve minimap2 alignment accuracy.
Bioinformatics. 2021 Oct 8:btab705. doi: 10.1093/bioinformatics/btab705. Epub ahead of print. PMID: 34623391.

Li H.
Minimap2: pairwise alignment for nucleotide sequences.
Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PMID: 29750242; PMCID: PMC6137996.