Difference between revisions of "GBrowse syn Database"

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(Parse the alignments)
(How the alignment data loading format=)
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* The output of this script is described below
 
* The output of this script is described below
  
=How the alignment data loading format==
+
===alignment data loading format===
 
* The output of the script is a tab-delimited ''ad hoc'' intermediate format that encodes the alignment coordinates plus 1:1 mapping of coordinates within the alignment (to facilitate accurate grid-lines in GBrowse_syn)
 
* The output of the script is a tab-delimited ''ad hoc'' intermediate format that encodes the alignment coordinates plus 1:1 mapping of coordinates within the alignment (to facilitate accurate grid-lines in GBrowse_syn)
 
* However to get you alignment or syntency data, this the the format currently supported for loading the alignment database.
 
* However to get you alignment or syntency data, this the the format currently supported for loading the alignment database.

Revision as of 10:59, 27 April 2009

GBrowse_syn is a GBrowse based synteny viewer. This page describes the database that GBrowse_syn uses, and how to get syntenic data into that database.

Schema

  • The alignment database schema is very simple; it has a tables for all reciprocal 'hits', or alignment features and a table for (optional) 1:1 coordinate maps
  • The alignments table contains coordinate information and also support cigar-line representations and the alignment to facilitate future reconstruction of the alignment within GBrowse_syn.

GBS Schema.png

Sample data

Loading

  • The starting point for loading the alignment database is a CLUSTALW format multiple sequence alignment
  • The source of the alignment data is up to you but the supported format for entry is currently CLUSTALW. This format is not mandatory but the parsing script below will need to be adjusted to support other formats

Clustal alignment format

CLUSTAL W(1.81) multiple sequence alignment


c_briggsae-chrII(+)/43862-46313           ATGAGCTTCCACAAAAGCATGAGCTTTCTCAGCTTCTGCCACATCAGCATTCAAATGATC
c_remanei-Crem_Contig172(-)/123228-124941 ATGAGCCTCTACAACCGCATGATTCTTTTCAGCCTCTGCCACGTCCGCATTCAAATGCTC
c_brenneri-Cbre_Contig60(+)/627772-630087 ATGAGCCTCCACAACAGCATGATTTTTCTCGGCTTCCGCCACATCCGCATTCAAATGATC
c_elegans-II(+)/9706834-9708803           ATGAGCCTCTACTACAGCATGATTCTTCTCAGCTTCTGCAACGTCAGCATTCAGATGATC
                                          ****** ** ** *  ******   ** ** ** ** ** ** ** ******* *** **

c_briggsae-chrII(+)/43862-46313           CGCACAAATATGATGCACAAATCCACAACCTAAAGCATCTCCGATAACGTTGACCGAAGT
c_remanei-Crem_Contig172(-)/123228-124941 AGCACAAATGTAATGAACGAATCCGCATCCCAACGCATCGCCAATCACATTCACAGATGT
c_brenneri-Cbre_Contig60(+)/627772-630087 CGCACAAATGTAGTGGACAAATCCGCATCCCAAAGCGTCTCCGATAACATTTACCGAAGT
c_elegans-II(+)/9706834-9708803           TGCACAAATGTGATGAACGAATCCACATCCCAATGCATCACCGATCACATTGACAGATGT
                                           ******** *  ** ** ***** ** ** ** ** ** ** ** ** ** ** ** **
c_briggsae-chrII(+)/43862-46313           CCGGAGTCGATCCCTGAAT-----------------------------------------
c_remanei-Crem_Contig172(-)/123228-124941 ACGAAGTCGGTCCCTATAAGGTATGATTTTATATGA----TGTACCATAAGGAAATAGTC
c_brenneri-Cbre_Contig60(+)/627772-630087 ACGAAGTCGATCCCTGAAA---------TCAGATGAGCGGTTGACCA---GAGAACAACC
c_elegans-II(+)/9706834-9708803           ACGAAGTCGGTCCCTGAAC--AATTATTT----TGA----TATA---GAAAGAAACGGTA
                                           ** ***** *****  *

NOTE: The sequence naming convention "species-seqid(strand)/start-end" shown in the above example is essential for the data to be loaded correctly

Database Loading Scripts

Split large clustal files into smaller ones

Split large clustal files into one alignment/file with the script split_clustal.pl. This is necessary for very large files that would otherwise overload the BioPerl alignment parser.

gunzip my_huge_clustal_file.aln.gz | perl split_clustal.pl /path/to/smaller_alignment_files

Parse the alignments

A suggested method for formatiing alignment data is to parse clustalw format the alignments using the script clustal2hits.pl

perl clustal2hit.pl /path/to/smaller_alignment_files/*.aln |gzip -c >processed_alignments.txt.gz
  • The output of this script is described below

alignment data loading format

  • The output of the script is a tab-delimited ad hoc intermediate format that encodes the alignment coordinates plus 1:1 mapping of coordinates within the alignment (to facilitate accurate grid-lines in GBrowse_syn)
  • However to get you alignment or syntency data, this the the format currently supported for loading the alignment database.
  • Each record is a single line (wrapped here for display only)
#species1       seqid1  start1   end1   strand1  reserved  species2      seqid2         start2   end2  strand2 reserved \
# pos1-1  pos1-2  ...  posn-1  posn-2  |  pos1-2  pos1-1  ...  posn-2  posn-1
c_briggsae      chrI    1583997 1590364 +       .       c_remanei       Crem_Contig24   631879  634679  -       .       \
1584000 634676  1584100 634584  (truncated for display...)  |     631900  1590333 632000  1590233  (truncated for display...)

Create a mysql database

mysql -uroot -ppassword -e 'create database my_database'

Load the database

load the database with the script load_alignment_database.pl

gunzip -c processed_alignments.txt.gz | perl load_alignment_database.pl
  • Once loaded, the data look something like this:

The alignment data Alignments table.png

The grid mapping data
Grid map.png