Evolutionary age

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Revision as of 05:26, 14 August 2010 (view source) Igchoi (Talk | contribs) (→Tree data) ← Older edit		Revision as of 06:19, 16 August 2010 (view source) Igchoi (Talk | contribs) (→Pfam data (24.0)) Newer edit →
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	*Loading into MySQL		*Loading into MySQL
	**Not all DBs were imported (only a few key DBs for this study)		**Not all DBs were imported (only a few key DBs for this study)
-	**pfamseq, genome_seqs, ncbi_taxonomy, genome_species, pfamA, gene_ontology	+	**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"
		+	<pre>
		+	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. </pre>
	<pre>		<pre>
	mysql -u user -p		mysql -u user -p

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Revision as of 06:19, 16 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(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 &

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?

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)