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

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