> This is why you will get different results/scores if you search a > sequence against a full database and then repeat the same search agains= t > a segment or smaller piece of the full database. Yeah, I understand. > Back in the old days of bioinformatics :) getting around this problem > used to be a giant pain in the ass and involved manually parsing out an= d > correcting all of the scores from your segmented blast results. It was > doable but the process was open to parsing and statistical errors and > was just Not Fun. Ooops, I forget this, I'm a newbie. In fact, I'm a computer science *stud= ent*=20 making some "research" in my summer time (yeah, we are in summer here)=20 without any knowledge about biologist, so I don't unknow the old days of=20 bioinformatics ;-) ... Im learning with falls .. but I have so many desir= e to=20 learn more .. what am I do here ? just learning ... [you may take this as= a=20 joke, but is true] I made some scripts in Perl to parsing the results/scores of each piece f= rom=20 the splitted "nt" database. I get the bests of each results and compare e= ach=20 other to choose the best of the best (I hope you understand this) Example (dummy values) three pieces of nt databse for one sequence: result1 -> VVCCSSA01.g -> Score =3D 12, Score =3D 10, etc .. result2 -> VVCCSSA01.g -> Score =3D 16, Score =3D 14, etc=20 result3 -> VVCCSSA01.g -> Score =3D 20, Score =3D 18, etc So .. I chose from result 1 --> Score =3D 12 (the best, maximum), Score =3D= 16=20 from result 2, Score =3D 20 from result3 ... then I compare and I choose = Score=20 =3D 18 from result 3 as my result. But statistical errors are not right, because I am reducing my search spa= ce as=20 you say. > o Added the "-z" option to explicitly ovverride the effective length > of the database (added in blast release 2.0.4) > o XML output option (added in blast release 2.1.2) Aha ! I don't know -z option, maybe I have some older versions of blast. XML ? I don't like it :) [... -z option versus XML] So as you see .. I have to read and learn more .. I will test your ideas = and=20 comments for enhance my scripts. Thanks a lot ! > --Chris -- Sergio Ahumada N san@inf.utfsm.cl