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-	{|align="left" cellpadding="15"	+	{|align="left" cellpadding="25"
	| __TOC__		| __TOC__
	|}		|}
-	==Evolutionary age of protein domains==	+	=Evolutionary age of protein domains=
	(Based on this reference)		(Based on this reference)
	<biblio>Reference pmid=16959887</biblio>		<biblio>Reference pmid=16959887</biblio>
-	===Pfam data (24.0)===	+	==Data==
		+	===Pfam release 24.0 (2009. Oct)===
	*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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	*[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
	*Genus (taxonomy): 31,949		*Genus (taxonomy): 31,949
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	</pre>		</pre>
	*Now, you have a list of Pfam having taxonomic distribution (ready to map)		*Now, you have a list of Pfam having taxonomic distribution (ready to map)
-	====Building the universal phylogenetic tree====	+	===Building the universal phylogenetic tree===
	===Procedure===		===Procedure===

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Revision as of 13:43, 16 August 2010

Contents 1 Evolutionary age of protein domains 1.1 Data 1.1.1 Pfam release 24.0 (2009. Oct) 1.1.2 Tree data 1.2 Results 1.2.1 Building the universal phylogenetic tree 1.2.2 Procedure

Evolutionary age of protein domains

(Based on this reference)

1. Error fetching PMID 16959887: [Reference]

Data

Pfam release 24.0 (2009. Oct)

• 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(not available), ncbi_taxonomy, genome_species(not availabe), pfamA, gene_ontology
  • Release 24 - pfamseq, pfamA, ncbi_taxonomy, taxonomy, pfamA_reg_full_significant
    • in_full should "1"

The pfamA_reg_full_significant and pfamA_reg_full_insignificant tables contain,
as the names suggest, the significant and insignificant data respectively.
Significant hits are those with a bits score above the curated threshold for the family,
whilst insignificant matches are those that score below the curated threshold.
With respect to the tables that contain significant data (pfamA_reg_full_significant and
pfamA_reg_full), there is an extra column called 'in_full'.
The matches that are present in the full alignment for a Pfam family have this column set to 1,
while those that are not present in the full alignment have the 'in_full' column set to 0.
Where there is an overlapping fragment match and a full length match to the same Pfam-A family, only one of the matches will be present in the full alignment for that Pfam-A family. 

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 &

• using R to analyze taxonomic distribution
  • see which fields should be used to link the databases...

Tree data

• Silva: SSU rRNA database

Results

• Species in Pfam (NCBI taxonomy): 148,925 species
• Genus (taxonomy): 31,949
  • taxonomy - browsing order in the web?
• MySQL query for the taxonomic distribution retrieval
  • pfamseq, pfamA, pfamA_reg_full_significant

# pfamA list
select distinct pfamA_id, auto_pfamA FROM pfamA;
# protein sequences of each auto_pfamA (pfamA_id)
select auto_pfamseq from pfamA_reg_full_significant WHERE auto_pfamA = '';
# taxonomic distribution
SELECT DISTINCT species,taxonomy,ncbi_code FROM pfamseq WHERE auto_pfamseq = 'auto_pfamseq';

or

SELECT DISTINCT species, taxonomy, ncbi_code FROM pfamseq seq, pfamA pf, pfamA_reg_full_significant sig \
       WHERE pf.pfamA_id='PF...' \
       AND sig.auto_pfamA=pf.auto_pfamA \
       AND seq.auto_pfamseq=sig.auto_pfamseq;

• Now, you have a list of Pfam having taxonomic distribution (ready to map)

Building the universal phylogenetic tree

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)