Sequence Databases on PMGM


We have a variety of databases locally. If you can find the sequence in a local database, it will be easier to download in a format that GCG or Intelligenetics can handle.

Some of the local databases include

Database

Contents

GCG Program To Use

Genbank

GenBank Nucleic Acid Database

FASTA, TFASTA, LOOKUP

PIR

PIR Protein Database

FASTA, LOOKUP

SwissProt

SwissProt Protein Database

FASTA, LOOKUP

GenPept

Translation of GenBank ORFs

FASTA

REBASE

Restriction Enzyme Database

MAP

TFD

Transcription Factor Database

FindPatterns, MAP

Prosite

Protein Motifs

Motifs

BLOCKS

Protein Motifs

blimps

PDB

3D Molecular Coordinates

Itidis

Currently, a new version of GenBank is released every 2 months (Aug 15, Oct 15, etc). We get all the sections of GenBank except for the ESTs and the STS databases. If you want to search those sections, visit the NCBI Blast Site or do a GCG Blast search

GenBank is divided into different sections

GenBank Subset

Contents

gb_ba

Bacterial Sequences

gb_in

Invertebrates including drosophila and C. elegans

gb_new

New Sequences since last full release

gb_om

Other Mammalian

gb_ov

Other Vertebrate Not Listed Above

gb_pat

Patented Seqeunces

gb_ph

Phage Seqeunces

gb_pl

Plant Sequences including Yeast, Algae, Arabadopsis

gb_pr

Primate sequences including Human

gb_ro

Rodent Sequences

gb_sy

Synthetic Sequences including Cloning Vectors

gb_st

Structural, like Ribosomal RNA

gb_vi

Viral Sequences

yeast

Yeast Genome

The GenPept database of translations of GenBank ORFs is named like the corresponding Genbank database files, except the "gb" is replaced with "gp" as shown below

GenPept Subset

Contents

gp_ba

Bacterial Sequences

gp_in

Invertebrates including drosophila and C. elegans

In GCG, if you want to search a specific database subset, all you have to do is enter the name of the database when requested, for example

What Database to Search ? gb_ro:*

Putting a ":*" after the name of the database will search all the sequences within that database.

If you only want to search part of the database, for example, only the "human" subset of the primate database, then you can specify that part if you know prefix of the Locus Name of the sequences you want.

For example, entering

gb_pr:HUM*

Will search only the human subset of the primate database.


Software

GCG

Databases

Web

Help

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