small RNA学习（三）：参考序列下载

0. 背景知识

非编码RNA介绍——百度词条

miRNA的命名规则：

详细介绍见https://mp.weixin.qq.com/s/SnrUB8v0_Mzlg2f4nHju3Q

1. 下载序列

Ensembl Plants
Favourite genomes中可以直接找到拟南芥

下载基因组序列及注释，和genes, cDNAs, ncRNA等序列。

Arabidopsis_thaliana.TAIR10.42.gff3.gz
Arabidopsis_thaliana.TAIR10.cdna.abinitio.fa.gz
Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz
Arabidopsis_thaliana.TAIR10.cds.all.fa.gz
Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
Arabidopsis_thaliana.TAIR10.ncrna.fa.gz
Arabidopsis_thaliana.TAIR10.pep.abinitio.fa.gz
Arabidopsis_thaliana.TAIR10.pep.all.fa.gz

$ less Arabidopsis_thaliana.TAIR10.42.gff3.gz | grep "^#" -v | cut -f3 | sort | uniq -c
 286067 CDS           7 chromosome
 313952 exon      56384 five_prime_UTR
  27655 gene       3879 lnc_RNA
    325 miRNA     48359 mRNA
    377 ncRNA      5178 ncRNA_gene
     15 rRNA        287 snoRNA
     82 snRNA      48308 three_prime_UTR
    689 tRNA

2. 非编码RNA数据库

2.1 PNRD

中国农业大学开发，http://structuralbiology.cau.edu.cn/PNRD/download.php
数据方便下载，但是似乎没有更新了。

下载拟南芥所有非编码RNA序列和靶标信息。

$ ll
total 24M
-rw-r--r-- 1 huangsiyuan grp3 2.9M Jan 19 11:41 lncRNA.txt
-rw-r--r-- 1 huangsiyuan grp3  64K Jan 19 11:40 miRNA.txt
-rw-r--r-- 1 huangsiyuan grp3  26K Jan 19 11:41 snoRNA.txt
-rw-r--r-- 1 huangsiyuan grp3 8.5K Jan 19 11:42 snRNA.txt
-rw-r--r-- 1 huangsiyuan grp3 233K Jan 19 11:40 stem_loop.txt
-rw-r--r-- 1 huangsiyuan grp3  21M Jan 19 11:44 tar.txt
-rw-r--r-- 1 huangsiyuan grp3  948 Jan 19 11:42 tasiRNA.txt
-rw-r--r-- 1 huangsiyuan grp3  67K Jan 19 11:42 tRNA.txt

看看自己下载的序列

$ head -n 6 miRNA.txt #成熟的miRNA序列
>ath-miR156a
UGACAGAAGAGAGUGAGCAC
>ath-miR156b
UGACAGAAGAGAGUGAGCAC
>ath-miR156c
UGACAGAAGAGAGUGAGCAC
huangsiyuan 13:57:16 ~/learn_rnaseq/srna_project/ref_ncrna
$ head -n 6 stem_loop.txt #茎环结构序列
>ath-MIR156a
CAAGAGAAACGCAAAGAAACUGACAGAAGAGAGUGAGCACACAAAGGCAAUUUGCAUAUCAUUGCACUUGCUUCUCUUGCGUGCUCACUGCUCUUUCUGUCAGAUUCCGGUGCUGAUCUCUUU
>ath-MIR156b
GCUAGAAGAGGGAGAGAUGGUGAUUGAGGAAUGCAACAGAGAAAACUGACAGAAGAGAGUGAGCACAUGCAGGCACUGUUAUGUGUCUAUAACUUUGCGUGUGCGUGCUCACCUCUCUUUCUGUCAGUUGCCUAUCUCUGCCUGCUUGACCUCUCUCUCUCUCUCUCUCUCUCAAAUUUGGCU
>ath-MIR156c
CGCAUAGAAACUGACAGAAGAGAGUGAGCACACAAAGGCACUUUGCAUGUUCGAUGCAUUUGCUUCUCUUGCGUGCUCACUGCUCUAUCUGUCAGAUUCCGGCU
两个文件的顺序是对应的

茎环序列不一样也能产生高度相似的成熟miRNA