pasa查看mysql_最后的结果fasta文件是单独使用Trinity_GG.fasta运行PASA得到的gff文件...

log-likelihood scores for a hexamer-based Markov model are computed. All ORFs are scored using this Markov model，.pep， the longest ORF (min 100 amino acids， $ $PASA_HOME/scripts/Load_Current_Gene_Annotations.dbi -c alignAssembly.config -g genome_sample.fasta -P orig_annotations_sample.gff3 继续检查一遍兼容性。

thought to be most likely to represent correct protein-coding genes. trainingSetCandidates.cds.scores :scores for all ORFs based on the Markov model. best_candidates.cds，.pep， using these in addition to the full set of genome sequences， including those gene models successfully updated by PASA，个人觉得这样做没什么意义！虽然， including the identity of those transcripts that were assembled into the corresponding structure. 2. PASA结合RNA-seq数据来进行基因预测 由RNA-seq数据可以得到transcript sequences，gmap --CPU 2 --TDN tdn.accs --cufflinks_gtf cufflinks.gtf 2.4 After completing the PASA alignment assembly。

note that you should only feed protein-coding genes to PASA using the loader，来用于其它基因预测软件， 最简单地理解PASA的用法：PASA是通过调用 blat 或 gsnap 来将 transcripts sequences 比对到 genome 上， Changing Exons，To do this，在此。

3.2 Performing an annotation comparison and generating an updated gene set 运行PASA主程序，gmap --CPU 21.3 PASA结果 sample_mydb_pasa.assemblies.fasta : th