GenScalpel 1.1 – Retrieve and Extract DNA or Protein sequence from NCBI GenBank file

GenScalpel 1.1

:: DESCRIPTION

GenScalpel is a program designed for specified-sequence retrieval and extraction from large-scale sequence sets in NCBI GenBank flatfile format.

::DEVELOPER

GenScalpel team

:: SCREENSHOTS

GenScalpel

:: REQUIREMENTS

  • Windows / Linux
  • Perl

:: DOWNLOAD

 GenScalpel

:: MORE INFORMATION

Citation

J Hered. 2012 Nov-Dec;103(6):908-11. doi: 10.1093/jhered/ess052. Epub 2012 Sep 2.
GenScalpel: an application for sequence retrieval and extraction from the GenBank flatfile.
Yin YH, Du LM, Yue BS.

Sequin 15.10 – Submit & Update Entries to the GenBank Sequence Database

Sequin 15.10

:: DESCRIPTION

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank,  EMBL, and DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, gapped sequences, or phylogenetic and population studies.

::DEVELOPER

the National Center for Biotechnology Information

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Sequin

:: MORE INFORMATION

ARBitrator 1.0 – Retrieval of auto-curated nifH sequences from GenBank

ARBitrator 1.0

:: DESCRIPTION

ARBitrator is a pipeline for automated retrieval from GenBank of all sequences for a specified gene.

::DEVELOPER

Zehr Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 ARBitrator

:: MORE INFORMATION

Citation:

ARBitrator: A software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank.
Heller P, Tripp HJ, Turk-Kubo K, Zehr JP.
Bioinformatics. 2014 Jul 2. pii: btu417

PubCrawler 2.16 – Update Alerting Service for PubMed and GenBank

PubCrawler 2.16

:: DESCRIPTION

PubCrawler is a free “alerting” service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases.  PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests.

::DEVELOPER

Ken Wolfe’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 PubCrawler

:: MORE INFORMATION

GBKParser 201103 – Parsing basic Gene Information from a Genbank file

GBKParser 201103

:: DESCRIPTION

GBKParser, a simple tool for parsing basic gene information from a genbank file.

::DEVELOPER

GEMSiRV team

:: SCREENSHOTS

GBKParser

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GBKParser

:: MORE INFORMATION

Genetic Revision – Searching Information in GenBank

Genetic Revision

:: DESCRIPTION

Genetic Revision (previously search GenBank) system and web portal allows searching information in GenBank and also in other NCBI databases through the interactive orchestration of NCBI Web services.

::DEVELOPER

Dariusz Mrozek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • PHP
  • Apache 2.2.10 or higher,
  • MySQL 5.1.30 or higher,

:: DOWNLOAD

 Genetic Revision

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Mar 1;14:73. doi: 10.1186/1471-2105-14-73.
search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information.
Mrozek D1, Małysiak-Mrozek B, Siążnik A.

AutoSequin – automatically Annotate Sequences for Bulk Submission to GenBank

AutoSequin

:: DESCRIPTION

AutoSequin is designed to speed up the process of submitting HIV sequences to GenBank via NCBI’s Sequin program. It is ideal for the batch sequence submission. It makes a special formated table required for running NCBI’s tbl2asn program to generate .sqn file for submission to GenBank.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 AutoSequin

:: MORE INFORMATION

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

GenBank2Treedyn 21 – Extract Annotations from GenBank Files

GenBank2Treedyn 21

:: DESCRIPTION

GenBank2Treedyn etract annotations from GenBank files for:
More convenient alignments and phylogeny (replace def line of fasta file by GI number)
Extremely powerfull annotations of phylogenetic trees with TreeDyn.

::DEVELOPER

Virtual Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 GenBank2Treedyn

:: 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.