BLAST Question - Scoring (Oct/05/2006 )
I am puzzled by some recent blast results. A submitted sequence has homology to hundreds of different NCBI phytoplasma sequences, but the way they are ranked is confusing.
Why aren't the matches at positions 16, 17, and 24, which have 2 long red [higher-scoring] segments ranked higher than the rest? Particularly the match at position 7, which has only one long and one very short green segment?
I would be happy to supply the sequence in question if anyone cares to try blasting it themselves. Thanks for any help you can offer.
They are ranked by E scores, which are only crudely represented by the colors of the bars. While I can't look, I would guess that the quality of the match of the longer fragment is substantially poorer than the quality of the match of the top scoring, shorter fragments.
and you are talking about sequence identity not homology.
Things are homologous or not - you cannot have 95% homology you can however have 95% identity.
One of my pet peeves. I am constantly correcting this in papers and such...
Things are homologous or not - you cannot have 95% homology you can however have 95% identity.
Hi,
I am a novice in this area and would like to know difference between homology and identity in DNA sequences.
there is another thread on the forum talking about this - have a look using the search function.
http://www.protocol-online.org/forums/inde...showtopic=20861
Greek homeos = identical and logos = word