Evolutionary age

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(→Evolutionary age of protein domains)
(→Pfam release 24.0 (2009. Oct))
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mysql>load data local infile 'pfamseq.txt' into table pfamseq FIELDS ENCLOSED BY "\'";
mysql>load data local infile 'pfamseq.txt' into table pfamseq FIELDS ENCLOSED BY "\'";
</pre>
</pre>
-
*MySQL로 로딩시, 테이블 작성 순서대로 할것 - 에러발생 (작성하지 않은 테이블의 키인덱스 링크 [http://dev.mysql.com/doc/refman/5.1/en/innodb-foreign-key-constraints.html 관련 키워드])
+
====MySQL====
 +
*[[MySQL]]로 로딩시, 테이블 작성 순서대로 할것 - 에러발생 (작성하지 않은 테이블의 키인덱스 링크 [http://dev.mysql.com/doc/refman/5.1/en/innodb-foreign-key-constraints.html 관련 키워드])
**loading time: a few hours
**loading time: a few hours
*Loading data file in background job
*Loading data file in background job
 +
*Need to tune the database parameters <- it is very critical to process the calculation
 +
**innodb_buffer_pool_size
 +
**query_cache
 +
**query_buffer
<pre>
<pre>
mysql -u user -p'passwd' database < loadscript.sql &
mysql -u user -p'passwd' database < loadscript.sql &
</pre>
</pre>
 +
====R====
*using [[R]] to analyze taxonomic distribution
*using [[R]] to analyze taxonomic distribution
**see which fields should be used to link the databases...
**see which fields should be used to link the databases...

Revision as of 01:29, 17 August 2010

Contents

Evolutionary age of protein domains

(Based on this reference)

Error fetching PMID 16959887:
  1. Error fetching PMID 16959887: [Reference]

Data

Pfam release 24.0 (2009. Oct)

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

MySQL

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

R

Tree data

Results

# 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;

Building the universal phylogenetic tree

Procedure

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