蛋白分析

Gi：40644130 allene oxide cyclase 【Niootiana tabacum】

丙二烯氧化环化酶(allene oxide cyclase, AOC)

Gi：140083805 cytosolic class II small heatshock protein HSP17.5 【Rosa hybrid cultivar】

Gi：289487897 Lasoorbate peroxidasa 【Bruguiera gymnorhiza】

比如是核糖体16S, 18S，或ITS等DNA序列，一般在Blast n 中搜索，到底是用megablast，discontiguous megablast还是blastn要根据你的序列与数据库序列的相似性，一般首先用blastn，它对相似性要求较低，可发现大量相似序列，如果进一步要求，再选择megablast 等。但是注意blastn搜索数据库对核酸序列相似性要求较高，如果序列保守性不高，比如新的RNA病毒的基因组序列，可能很难得到结果，这时需要用blastp 或Blast x等。

如果是编码蛋白的基因序列，可先将其翻译成蛋白（注意，一条序列理论上有六种编码可能）然后分别去blastp搜索蛋白数据库，当然，你也可直接将其在Blast x中搜索，Blast x会自动将六种编码可能分别翻译后搜索蛋白数据库。

Blastp/PSI-Blast/PHI-BLAST都是蛋白序列与蛋白序列之间的Blast比对。

1，Blastp: 标准的蛋白序列与蛋白序列之间的比对

Standard protein BLAST is designed for protein searches.

Blastp用于确定查询的氨基酸序列在蛋白数据库中找到相似的序列。跟其它的Blast程序一样，目的是要找到相似的区域。

2，PSI-BLAST : 敏感度更高的蛋白序列与蛋白序列之间的比对

PSI-BLAST is designed for more sensitive protein-protein similarity searches.

Position-Specific Iterated (PSI)-BLAST，是一种更加高灵敏的Blastp程序，对于发现远亲物种的相似蛋白或某个蛋白家族的新成员非常有效。当你使用标准的Blastp比对失败时，或比对的结果仅仅是一些假基因或推测的基因序列时（"hypothetical protein" or "similar to..."），你可以选择PSI-BLAST重新试试。

3，PHI-BLAST : 模式发现迭代BLAST

PHI-BLAST can do a restricted protein pattern search.

PHI-BLAST, 模式发现迭代BLAST, 用蛋白查询来搜索蛋白数据库的一个程序。仅仅找出那些查询序列中含有的特殊模式的对齐。

PHI的语法详细介绍看这里：/blast/html/PHIsyntax.html

The syntax for patterns in PHI-BLAST follows the conventions of PROSITE. When using the stand-alone program, it is permissible to have multiple patterns in a file separated by a blank line between patterns. When using the Web-page only one pattern is allowed per query.

Valid protein characters for PHI-BLAST patterns:

ABCDEFGHIKLMNPQRSTVWXYZU

Valid DNA characters for PHI-BLAST patterns:

ACGT

Other useful delimiters:

[ ] means any one of the characters enclosed in the brackets e.g., [LFYT] means one occurrence of L or F or Y or T

- means nothing (this is a spacer character used by PROSITE)

x(5) means 5 positions in which any residue is allowed (and similarly for any other single number in parentheses after x)

x(2,4) means 2 to 4 positions where any residue is allowed, and similarly for any other two numbers separated by a comma; the first number should be < the second number. can occur only at the end of a pattern and means nothing it may occur before a period (another spacer used by PROSITE) may be used at the end of the pattern and means nothing.

When using the stand-alone program, the pattern should be in a file, with the first line starting:

ID followed by 2 spaces and a text string giving the pattern a name. There should also be a line starting PA followed by 2 spaces followed by the pattern description.

All other PROSITE codes in the first two columns are allowed, but only the HI code, described below is relevant to PHI-BLAST.

Here is an example from PROSITE.

ID CNMP_BINDING_2; PATTERN.

AC PS00889;

DT OCT-1993 (CREATED); OCT-1993 (DA TA UPDA TE); NOV-1995 (INFO UPDATE).

DE Cyclic nucleotide-binding domain signature 2.

PA [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].

NR /RELEASE=32,49340;

NR /TOTAL=57(36); /POSITIVE=57(36); /UNKNOWN=0(0); /FALSE_POS=0(0);

NR /FALSE_NEG=1; /PARTIAL=1;