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

GenomeSlicer 1.1 – Extracts Relevant Sub-sequences from Fasta or Genbank format Sequence Files

GenomeSlicer 1.1

:: DESCRIPTION

GenomeSlicer is a graphical tool for Microsoft Windows which extracts relevant sub-sequences from Fasta or Genbank format sequence files. GenomeSlicer can return targeted coding sequences (genes), variable regions upstream or downstream of genes, as well as sub-sequences specified by a given 5′ coordinate and 3′ coordinate. GenomeSlicer can generate output in both multi-fasta and spreadsheet formats.

::DEVELOPER

Elliot Nierman (enierman@gmail.com) at The Institute For Genomic Research (TIGR)

:: SCREENSHOTS

GenomeSlicer

:: REQUIREMENTS

  • Windows
  • Excel

:: DOWNLOAD

 GenomeSlicer

:: MORE INFORMATION

Database Manager 2.1 – FASTA Database Manager

Database Manager 2.1

:: DESCRIPTION

Database Manager stores all your sequence databases in a single folder (repository). It offers :

  • conservation of metadata : database origin, species, number of protein, download site, …
  • translation of DNA into protein
  • creation of decoy protein databases (protein reverse, random, peptide reverse
  • combination of different existing databases

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

Fastamanager

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 Database Manager

:: MORE INFORMATION

sff_extract 0.3.0 – Extract the reads from the sff files into Fasta / xml/ caf file

sff_extract 0.3.0

:: DESCRIPTION

sff_extract extracts the reads from the sff files and stores them into fasta and xml or caf text files. 454 sequence reads are usually stored in sff files. In these files the information about the reads is stored: sequence, quality and quality and adapter clips.

::DEVELOPER

Jose Blanca and Bastien Chevreux @ Bioinformatics at COMAV 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 sff_extract

:: MORE INFORMATION

FASTA BLAST Scan 2.4 – FASTA & BLAST Alignment Conversion

FASTA BLAST Scan 2.4

:: DESCRIPTION

FASTA BLAST Scan is a program for processing nucleotide sequences alignment made with FASTA and BLAST alignment tools.

::DEVELOPER

Olivier Friard

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FASTA BLAST Scan

:: MORE INFORMATION

FASTA BLAST Scan is released under the GNU General Public License (GPL)

Genbank_to_Fasta 1.1 – Genbank/EMBL to FASTA Conversion Tool

Genbank_to_Fasta 1.1

:: DESCRIPTION

Genbank_to_Fasta is designed to accept a GenBank or EMBL format file, and convert it to a FASTA file. You have control over what kind of sequence gets extracted, and how the header line is written. Select a GenBank or EMBL format file to upload containing a feature table. Select the file format. Choose the delimiter characters that will separate the qualifiers from one another in the header line. Select whether to extract translated amino acid sequences, DNA sequence for each feature, or the entire DNA sequence of the whole record. To choose how your header line appears, designate the names of the qualifiers, one per field, in the order that you want them to appear in the FASTA header line.

::DEVELOPER

the Rocap lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Python

:: DOWNLOAD

 Genbank_to_Fasta

:: MORE INFORMATION

FastaGrep 2.0 – Search Oligonucleotide Binding Sites from FastA Genomic Sequences

FastaGrep 2.0

:: DESCRIPTION

FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. It can do both, match/mismatch based and thermodynamic binding energy searches.

::DEVELOPER

Department of Bioinformatics, University of Tartu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastaGrep

:: MORE INFORMATION

Vector NTI Viewer 4.0.1 – Read DNA Sequence Data from GenBank, EMBL or FASTA files

Vector NTI Viewer 4.0.1

:: DESCRIPTION

Vector NTI Viewer, a freeware program, allows scientists to study and analyze biological molecules. It incorporates a small subset of functions from the much more sophisticated Vector NTI Suite software.Vector NTI Viewer can read Vector NTI Molecule Documents, and molecule data from GenBank, EMBL or FASTA files. You may also paste molecule descriptions in one of the above formats from the Clipboard. In addition, the Viewer can read plain nucleotide sequence data form ASCII file or the Clipboard, automatically creating a virtual annotated molecule for that nucleotide sequence.

::DEVELOPER

Life Technologies

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Macintosh

:: DOWNLOAD

Vector NTI Viewer

:: MORE INFORMATION

The Vector NTI Viewer is free.

STORM 1.01 – Protein Analyses of BLAST, FASTA, Pfam and ProtParam

STORM 1.01

:: DESCRIPTION

STORM (Systematic Tailored Orf-data Retrieval & Management) combines protein analyses of BLAST, FASTA, Pfam and ProtParam on a batch-file of protein sequences. It subsequently summarizes and organizes the output in an Access database format.More specifically, STORM extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches (BLASTp and FASTA) as well as Pfam predictions and Protparam calculations of protein physicochemical properties.

::DEVELOPER

Laboratory of Gene Technology, Katholieke Universiteit Leuven

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft Access

:: DOWNLOAD

STORM

:: MORE INFORMATION

Citation

Lavigne, R., Sun, W.D. and Volckaert, G.
STORM towards protein function: Systematic Tailored ORF-data Retrieval and Managment.
Applied Bioinformatics (2003) 2(3): 177-179

ABI2FASTA 1.1.2 – ABI to FASTA converter

ABI2FASTA 1.1.2

:: DESCRIPTION

ABI2FASTA (ABI to FASTA Converter)  can batch convert multiple ABI chromatogram files to FASTA files, with a single click.ABI to FASTA Converter offers a great relief for molecular biologists that must convert hundreds or thousands of ABI/AB chromatogram files manually. With this automatic ABI to FASTA Converter you can convert hundreds of ABI chromatogram files in seconds. All with A SINGLE PUSH OF A BUTTON! Now the ABI to FASTA converter can also automatically trim low quality ends from your chromatograms

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ABI2FASTA

:: MORE INFORMATION

The free version allows you to convert a limited number of files. The registered version does not have this limitation. Purchase url.