pasa查看mysql_PASA的安装与使用

1. PASA简介

PASA, acronym for Program to AssembleSpliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

Note:

Combine genome and Trinity de novo RNA-Seq assemblies to generate a comprehensive transcript database.

2. PASA使用前的准备

2.1 Mysql数据库的准备

创建只读权限用户和所有权限用户各一个。mysql> GRANT SELECT ON *.* TO 'pasa'@'%' IDENTIFIED BY '123456';

mysql> GRANT ALL ON *.* TO 'chenlianfu'@'%' IDENTIFIED BY '123456';

mysql> FLUSH PRIVILEGES;

2.1 安装perl模块# cpan

cpan[1]> install DBD::mysql

cpan[1]> install GD

2.3 安装GMAP$ wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2013-03-31.v5.tar.gz

$ tar zxvf gmap-gsnap-2013-03-31.v5.tar.gz

$ cd gmap-2013-03-31

$ ./configure --prefix=$PWD

$ make -j 8

$ make install

2.4 安装BLAT$ wget http://hgwdev.cse.ucsc.e