发信人: feizj (cornell), 信区: Biology
标 题: Re: BLAST的一个问题
发信站: Unknown Space - 未名空间 (Thu Mar 11 17:37:29 2004) WWW-POST

【 在 vanLoon (壳壳龙) 的大作中提到: 】
: 比较小的protein, 比如phospholamban
(序列为MEKVQYLTRSAIRRASTIEMPQQARQKLQNLFINFCL
: ILICLLLICIIVMLL),现在想在Arabidopsis or rice genome里面找是否有homolog.试了
几次
: 都是没有结果的,包括concatenated都试过..
: 可能是短序列需要一些改变一下BLAST的参数,或者别的比较好的搜索engine?
: 请大家不吝指教.

You need to change default expect value (10) to a higher value. This is what I
got when blast against Arabidopsis proteins. But anyway, since the sequence is
too short, it's hard to find homologs from other species (confidence level is
low).


At1g26270.1 68414.m03205 phosphatidylinositol 3- and 4-kinase family
protein similar to phosphatidylinositol 4-kinase type-II
beta [Homo sapiens] GI:20159767; contains Pfam profile
PF00454: Phosphatidylinositol 3- and 4-kinase
Length = 630

Score = 23.1 bits (48), Expect = 26
Identities = 11/28 (39%), Positives = 17/28 (60%)

Query: 1 MEKVQYLTRSAIRRASTIEMPQQARQKL 28
+EK Q L AI + +I + Q+ RQ+L
Sbjct: 597 LEKYQELLYPAIEKRKSITLGQKQRQRL 624


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