sliva数据库简介--转载

sliva rRNA数据库（http://www.arb-silva.de/）用来检查和比对RNA序列，既可以针对16S/18S,SSU，也可以针对23S/28S, LSU，包括了Bacteria, Archaea and Eukarya。同时也是ARB的官方指定数据库。

LSU: Large subunit (23S/28Sribosomal RNAs)

SSU: Small subunit (16S/18Sribosomal RNAs)

1.下载

1.1 针对arb的下载

到目前（2015.2.4，最新的数据库为Realease119，网页版的已经到121版本了，但是现在不提供下载）

下载介绍http://www.arb-silva.de/download/arb-files/

下载地址：http://www.arb-silva.de/no_cache/download/archive/release_119/ARB_files/

我选择的是其中的 RefNR 99，他是Ref 119的无冗余版本。

wget –c 

http://www.arb-silva.de/fileadmin/silva_databases/release_119/ARB_files/SSURef_NR99_119_SILVA_14_07_14_opt.arb.tgz；

md5sum SSURef_NR99_119_SILVA_14_07_14_opt.arb.tgz；

wget –c ；http://www.arb-silva.de/fileadmin/silva_databases/release_119/ARB_files/SSURef_NR99_119_SILVA_14_07_14_opt.arb.tgz

 

1.2 仅仅是下载fasta文件

下载地址：http://www.arb-silva.de/no_cache/download/archive/release_119/Exports/

根据下载的需求，选择针对23S/28Sribosomal RNAs的LSU或者是针对16S/18Sribosomal RNAs的SSU；然后选择是否去冗余的，我选择去，即Nr99;然后选择是否trunc，即是否对名字缩写；选择是否全长比对结果；

*_tax_silva.fasta.gz

-----------------

Multi FASTA files of the SSU/LSU databases including the SILVAtaxonomy for

Bacteria, Archaea and Eukaryotes in the header.

REMARK: The sequences in the files are NOT truncated to theeffective LSU or

SSU genes. They contain the full entries as they have been depositedin the

public repositories (ENA/GenBank/DDBJ).

 

Fasta header:

>accession_number.start_position.stop_position taxonomic pathorganism name

 

*_tax_silva_full_align_trunc.fasta.gz

-----------------------

Multi FASTA files of the SSU/LSU databases including the SILVAtaxonomy for

Bacteria, Archaea and Eukaryotes in the header (including the FULLalignment).

REMARK: Sequences in these files haven been truncated. This meansthat all

nucleotides that have not been aligned were removed from thesequence.

 

*_tax_silva_trunc.fasta.gz

-----------------------

Multi FASTA files of the SSU/LSU database including the SILVAtaxonomy for

Bacteria, Archaea and Eukaryotes in the header.

REMARK: Sequences in these files haven been truncated. This meansthat all

nucleotides that have not been aligned were removed from thesequence.

 

生成使用与Mothur的silva数据库：http://blog.mothur.org/2014/08/08/SILVA-v119-reference-files/

 

文献：

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, PepliesJ, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improveddata processing and web-based tools. Opens external link in new windowNucl.Acids Res. 41 (D1): D590-D596