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Comparing popular database formats

Comparing popular database formats - Bioinformatics

Comparing popular database formats - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 09-02-2010, 06:50 AM
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Default 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
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Old 09-03-2010, 03:33 AM
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Default 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.
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Old 09-06-2010, 11:54 AM
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Default 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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