sliva rRNA數據庫（http://www.arb-silva.de/）用來檢查和比對RNA序列，既可以針對16S/18S,SSU，也可以針對23S/28S, LSU，包括了Bacteria, Archaea and Eukarya。同時也是ARB的官方指定數據庫。

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

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

1.下載

1.1?針對arb的下載

到目前（2015.2.4，最新的數據庫為Realease119，網頁版的已經到121版本了，但是現在不提供下載）

下載介紹http://www.arb-silva.de/download/arb-files/

下載地址：http://www.arb-silva.de/no_cache/download/archive/release_119/ARB_files/

我選擇的是其中的?RefNR 99，他是Ref 119的無冗余版本。

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?僅僅是下載fasta文件

下載地址：http://www.arb-silva.de/no_cache/download/archive/release_119/Exports/

根據下載的需求，選擇針對23S/28Sribosomal RNAs的LSU或者是針對16S/18Sribosomal RNAs的SSU；然后選擇是否去冗余的，我選擇去，即Nr99;然后選擇是否trunc，即是否對名字縮寫；選擇是否全長比對結果；

*_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.

?

生成使用與Mothur的silva數據庫：http://blog.mothur.org/2014/08/08/SILVA-v119-reference-files/

?

文獻：

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, PepliesJ, Gl?ckner 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

轉載于:https://www.cnblogs.com/nkwy2012/p/6396427.html

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