Tag: FASTA

GWFASTA – FASTA search in Eukaryotic and Microbial Genomes

GWFASTA

:: DESCRIPTION

GWFASTA (Genome Wise Sequence Similarity Search using FASTA) allows user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search

::DEVELOPER

GWFASTA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Issac, B. and Raghava, G. P. S.(2002)
GWFASTA: A server for FASTA search in Eukaryotic and Microbial genomes.
BioTechniques 33(3):548-556.

FASTA 36.3.8 – Sequence Comparison

FASTA 36.3.8

:: DESCRIPTION

FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

::DEVELOPER

William R. Pearson at the University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Mac OsX / Windows

:: DOWNLOAD

FASTA

:: MORE INFORMATION

Citation:

Pearson WR, Lipman DJ.
Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8.

DBToolkit 4.2.3 – Manipulating fasta Sequence Databases

DBToolkit 4.2.3

:: DESCRIPTION

The dbtoolkit application enables easy manipulation of fasta sequence database in a user-friendly environment. Sequence databases can be merged, shuffled, truncated, etc… Furthermore, for more experienced users, the Java API provides a well documented and easy-to-use environment for customized fasta database manipulations.

::DEVELOPER

Computational Omics and Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 DBToolkit

:: MORE INFORMATION

Citation

Martens et al.
DBToolkit: processing protein databases for peptide-centric proteomics.
Bioinformatics (2005) vol. 21 (17) pp. 3584-5

Faster2 0.31 – Extensible Tool for working with FASTA and FASTQ files

Faster2 0.31

:: DESCRIPTION

Faster2 is an extensible C++11 framework and program for efficient access and extraction of DNA sequences from FASTA and FASTQ files. It works with large file collections of raw as well as compressed data, and is based on the set of filters that can be organized into a pipeline. Faster2 performs input data indexing in order to accelerate all supported operations. It can be easily customized and extended with new filters, and its pipeline building sub-system can be incorporated into other tools. Faster2 is not a database system nor a data analytics tool. Its sole purpose is to simplify tedious operations that are part of everyday tasks performed routinely by bioinformaticians and computational biologists, and yet often require writing specialized text-processing scripts. +

::DEVELOPER

Jaroslaw Zola

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

 Faster2

:: MORE INFORMATION

FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat – Conversion between Tab-delimited files and FASTA/ FastQ Format

FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat

:: DESCRIPTION

FastaFormat: Convert tab-delimited files into fasta format. Includes a quality score safe option (-q) for converting quality score files.

FastQFormat: Convert tab-delimited sequence and quality score files into fastQ format.

UnFastaFormat: Convert fasta files into tab-delimited format. Includes a quality score safe option (-q) for converting quality score files.

UnFastQFormat: Convert fastq files into tab-delimited format. Outputs sequences and quality scores into separate files. Edits sequence titles. Support for NCBI and Illumina formats.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • Perl

:: DOWNLOAD

 FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat

:: MORE INFORMATION

Validate Fasta File 2.1.5053 – Parse Fasta file and return the number of proteins and number of Residues

Validate Fasta File 2.1.5053

:: DESCRIPTION

The Validate Fasta File utility is a Windows command-line application that will parse a Fasta file and return the number of proteins and number of residues in the file. Additionally, it will check the validity of the fasta file looking for common, known problems.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 4.0

:: DOWNLOAD

 Validate Fasta File utility

:: MORE INFORMATION

MFCompress 1.01 – Compression tool for FASTA and multi-FASTA files

MFCompress 1.01

:: DESCRIPTION

MFCompress is a compression tool for FASTA and multi-FASTA files. In comparison to gzip and applied to multi-FASTA files, MFCompress can provide additional average compression gains of almost 50%, i.e.,it potentially doubles the available storage, although at the cost of some more computation time.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 MFCompress

:: MORE INFORMATION

Citation

Armando J. Pinho, and Diogo Pratas.
“MFCompress: a compression tool for FASTA and multi-FASTA data.”
Bioinformatics 30.1 (2014): 117-118.DOI: dx.doi.org/10.1093/bioinformatics/btt594.

FASTX-Toolkit 0.0.14 – Short-Reads FASTA/FASTQ files Preprocessing

FASTX-Toolkit 0.0.14

:: DESCRIPTION

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs.However,It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome – manipulating the sequences to produce better mapping results.The FASTX-Toolkit tools perform some of these preprocessing tasks.

:: DEVELOPER

The Hannon laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  FASTX-Toolkit

:: MORE INFORMATION

FaBox 1.41 – Online FASTA Sequences Toolbox

FaBox 1.41

:: DESCRIPTION

FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as ARLEQUIN , TCS and MRBAYES . The toolbox is expected to grow on the basis of requests for particular services and converters in the future.

::DEVELOPER

Palle Villesen Fredsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • WebServer
  • PHP

:: DOWNLOAD

 FaBox

:: MORE INFORMATION

Citation

Villesen, P (2007),
FaBox: an online toolbox for fasta sequences,
Molecular Ecology Notes 7 (6), 965-968. doi:10.1111/j.1471-8286.2007.01821.x