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thelionphoenix 09-02-2010 06:50 AM

Comparing popular database formats
 
Can anyone point out the common similarities and differences between the most commonly used database formats in bioinformatics :-
  1. Genbank
  2. EMBL
  3. Fasta
  4. GCG
  5. NBRF

Thanks in advance

Anastasiya 09-03-2010 03:33 AM

Re: Comparing popular database formats
 
The common similarity: all formats contain sequence, and some kind of sequence name.

Differences are described on EMBL database site, for example.

mfursov 09-06-2010 11:54 AM

Re: Comparing popular database formats
 
Genbank and EMBL are very close internally.
Basically the only difference you will see at the first glance is 2 symbol prefix for every line in EMBL files and sequence offsets positioning: left of right side.

FASTA format is very simple to parse and compact and doesn't support annotations for sequence regions. Sometimes people store multiple sequence alignments in FASTA format to keep the result file small


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