strange behavior of results HSP coordinates


I’m testing the custom link out options of SequencerServer and spotted a strange behavior. I embedded the ‘matches’ and ‘hit_coordinates’ values in the link pointing to a genome browser, and it works fine for a single query search against a single database. When I search a query against three databases, and apply relatively stringent parameters (to limit the hit number and score), I got three single hits for three databases, respectively. When I check the links, I saw that all hit identifiers (‘matches’ values) are correct, but the three links share the same ‘hit_coordinate[1]’ value, but with three different ‘hit_coordinate[2]’ values, which makes two of the three links incorrect as they don’t have the right start coordinates. Is this something in my ‘customisation.rb’ settings, or a potential bug? If it’s in the ‘customisation.rb’, why it gets three ending coordinates right but not the three starting coordinates?

By the way, so far I’m very happy with SequenceServer, kudos to the developers for this awesome app! Maybe I have a small suggestion: will SequenceServer offer a bit more parsing options for the output, such as output tabular format, or some API for messing with the results to connect multiple HSPs, etc? Or maybe this kind of parsing could be taken under the hood as offering more parameters instead of just ‘matches’ and ‘hit_coordinates’?



I did a bit more testing with a single database. Looks like I’m having a similar problem with multiple hits in one database. All hit coordinates are messed up except for one hit. Is this something happening in the way ‘hit_coordinates’ are fetched?



Hi Ke,

This is most probably an issue with SS and not something on your end.
SS BLASTs to HTML, parses hit id and coordinate, prettifies the result
a bit and presents it to the user. Parsing HTML (via regexp) for
result data (hit id, coordinate, evalue, etc.) is flaky to be honest -
a lot could go wrong. I apologise that I can't look into it at the
moment and suggest a fix because of time constraints. But the good
news is this:

Last couple of days we changed this so SS now BLASTs to XML, gets all
data from XML, and then renders the HTML. This has allowed us to take
full control of the results and make it more intuitive, elegant and
add a graphical overview. As of this writing we are polishing this and
stress testing against all versions of BLAST+ starting 2.2.25. This
also means adding external link per hit would become easier and you
will have all parameters BLAST gives to play with. I wonder how you
would make use of anything other than hit id and coordinates though.
What do you mean by connecting multiple HSPs? What else would you want
to tweak in the results or see as a part of default offering?

Thus for the issue at hand, I would urge you to make a temporary fix
to your installation and / or wait for the upcoming release.

Ability to download XML and TSV (with the option to tweak columns you
want) is on our agenda, but mostly likely only in later releases.

-- Priyam

Thank you very much for the response, Priyam!

I think a graphic overview and the correct coordinates for stitching HSPs together would be awesome and more than enough for our purposes. So I’ll be patient and wait for the the next exciting release. Thanks again for this great app!