Wednesday, March 11, 2009

Domain: a compact local semi-independent folding unit presumed to have arisen by gene fusion & gene duplication events.Domains are not formed from contiguous region of amino acid sequence.They may be discrete entities joined by a flexible linking region of the gene & may also exchange chains with domain neighbours.The combination of domains within a protein determines its overall functions & stable structure.

Analogues: non-homologus proteins that have similar folding site which are believed to have arisen through converges evolution.

ORF: Open Reading Frame.A series of DNA codon including a 5' initiation codon & a 3' termination codon that encodes a putative( known) gene.A DNA sequence must contain a translation start codon(usually ATG) & not exhibit any of the stop codons (usually TAA,TAG,TGA) in phase with the ATG for quite some length(at least 300 nuclotides seperate the start & stop codon).

The ORFing protocols can probably correctly identify 85% of the protein coding regions.There are a variety of situations that frequently occur where a more sophisticated approach need to use.One such approach is taken by GenMark which include
  • finding very short proteins,
  • resolving ambiguous cases where overlapping ORFs are predicted in different reading frames.
  • to pinpoint the exact start codon(most distal ATG is not always the correct one).
Six Frame Translation: Translation of a stretch of DNA taking into account three forward translations and three reverse translations arising from three possible reading frames of an uncharacterised stretch of DNA.

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