Evolutionary age

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Revision as of 05:05, 14 August 2010 (view source) Igchoi (Talk | contribs) (→Data set) ← Older edit		Revision as of 05:05, 14 August 2010 (view source) Igchoi (Talk | contribs) (→Data set) Newer edit →
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	(Based on this reference)		(Based on this reference)
	<biblio>Reference pmid=16959887</biblio>		<biblio>Reference pmid=16959887</biblio>
-	===Data set===	+	===Pfam data (24.0)===
	*The [http://pfam.sanger.ac.uk Pfam] database		*The [http://pfam.sanger.ac.uk Pfam] database
	**ftp [ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/ current_release]		**ftp [ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/ current_release]
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	mysql -u user -p'passwd' database < loadscript.sql &		mysql -u user -p'passwd' database < loadscript.sql &
	</pre>		</pre>
-	---	+
-	*Tree data	+	===Tree data===
	**[http://www.arb-silva.de/ Silva]: SSU rRNA database		**[http://www.arb-silva.de/ Silva]: SSU rRNA database
		+
	===Results===		===Results===
	*Species in Pfam (NCBI taxonomy): 148,925 species		*Species in Pfam (NCBI taxonomy): 148,925 species

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Revision as of 05:05, 14 August 2010

Contents 1 Evolutionary age of protein domains 1.1 Pfam data (24.0) 1.2 Tree data 1.3 Results 1.4 Procedure

Evolutionary age of protein domains

(Based on this reference)

1. Error fetching PMID 16959887: [Reference]

Pfam data (24.0)

• The Pfam database
  • ftp current_release
  • User manual (the pfam format)
  • Tip: use Mysql dump <- easy to handle the content

# download total DB (estimated ~2 days)
wget -c ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/database.tar &

• Loading into MySQL
  • Not all DBs were imported (only a few key DBs for this study)
  • pfamseq, genome_seqs, ncbi_taxonomy, genome_species, pfamA, gene_ontology

mysql -u user -p
mysql>create DATABASE pfam24; \q
mysql -u user -p pfam24 < FULL_PATH/pfamseq.sql
mysql -u user -p
mysql>use pfam24
mysql>load data local infile 'pfamseq.txt' into table pfamseq FIELDS ENCLOSED BY "\'";

• MySQL로 로딩시, 테이블 작성 순서대로 할것 - 에러발생 (작성하지 않은 테이블의 키인덱스 링크 관련 키워드)
  • loading time: a few hours
• Loading data file in background job

mysql -u user -p'passwd' database < loadscript.sql &

Tree data

• • Silva: SSU rRNA database

Results

• Species in Pfam (NCBI taxonomy): 148,925 species
• Genus (taxonomy): 31,949

Procedure

• Extract the taxonomic origins of each protein
• Get the Taxonomy info. of each origin
• Non-redundant (NR) set of taxonomic origins
• Collect all Small Subunit (SSU) rRNA sequences of the NR set
• Build the universal tree of life using SSU sequences
• Mapping the each protein belonging to a given domain into the universal tree
• Check which node is the most recent common ancestor (MRCA) node
• Calculate the branch length between MRCA and LCA (last common ancestor)