gene prediction pipeline

augustus

use EST file

 blat -minIdentity=92 aphis_genome_scaffold_v3.1.fa aphis-unigene.idx.fna aphis-unigene.idx.psl
/home/soft/pslCDnaFilter -maxAligns=1 aphis-unigene.idx.psl aphis-unigene.idx.f.psl
/home/soft/augustus.2.5/scripts/blat2hints.pl –in=aphis-unigene.idx.f.psl –out=hints.E.gff

./augustusRun.pl /public/d_aphis/DNA_assembly/3.1fix/gene_predict/augustus aphis_genome_scaffold_v3.1.fa pea_aphid hints.E.gff 15

./augustusRun.py -i aphis_genome_scaffold_v3.1.fa -n pea_aphid -j hints.E.gff -s 35000000 &

# —– prediction on sequence number 3 (length = 1746996, name = AGO_S000003) —–




geneid:

./scripts/gffftablExport.pl aphis.geneid.model.gff3 aphis.geneid geneid





blast2go


-rw-r–r– 1 zhaoqy users 90672652 2010-10-15 gene2go
-rw-r–r– 1 zhaoqy users 19294682 2010-11-19 gene_ontology.1_2.obo.txt
shenzy@node11:/home/zhaoqy/dat/GO$ pwd
/home/zhaoqy/dat/GO
shenzy@node11:/home/zhaoqy/dat/GO$

java -Xms1024m -Xmx10240m -jar  /home/zhouzh/lib/b2g4pipe/blast2go.jar   -prop  /home/zhouzh/lib/b2g4pipe/b2gPipe.properties  -in  pde-blastp.xml -a  -out  pde-blast2go.goa

备注：需要更改配置文件，会调用mysql /home/zhouzh/lib/b2g4pipe/b2gPipe.properties
./GO_for_annotation.pl aphis-blast2go.goa.annot aphis-blast2go.goa.annot.out &
./GO_add_description.pl 2 aphis-blast2go.goa.annot.out /home/zhaoqy/dat/GO/gene_ontology.1_2.obo.txt aphis-blast2go.goa.annot.out.def

/home/shenzy/work_python_script_bak/GO_add_description.pl 2 Trim_unigene_sprot_nr_blast2go.goa.annot.out /home/shenzy/work_python_script_bak/GO/gene_ontology.1_2.obo.txt Trim_unigene_sprot_nr_blast2go.goa.annot.out.def

tBLASTnParser.pl aphis_geneid_fgenesh_augustus.pep.blast.xml aphis_geneid_fgenesh_augustus.pep.blast.m8

./blastm8GO.py -i aphisGFA-blast2go.goa.annot.out.def -j aphis_geneid_fgenesh_augustus.pep.blast.m8 -o aphisGFAblastm8GO.result

备注： 当是对NR库和swissprot等分别做了blast时，除寻找GO信息需要先把两个xml文件（m7)合并来做时，对于做注释则需要分开做，分别寻找最合适的，然后在统一到一个表格。
分别表明swiss prot-id      Nr-id  等
###########################
psl2gff3

shenzy@node5:/public/d_aphis/DNA_assembly/3.1fix$ /home/soft/augustus.2.5/scripts/blat2gbrowse.pl
Unknown option

/home/soft/augustus.2.5/scripts/blat2gbrowse.pl — convert blat file to gbrowse file

Usage: /home/soft/augustus.2.5/scripts/blat2gbrowse.pl blat.psl gbrowse.gff
Options:
    –estnames=file    output file with the names of the ESTs
    –source=name      identifyier in the source column





KOG database
COG.mappings.v8.3.txt 该文件包含基因名和对应的COG和KOG号，通过blast找到查询序列与基因名的对应关系，在对应到KOG号
ln -s /home/zhouzh/seqLib/KOG/COG.mappings.v8.3.txt