BIP-Align Step 4 - Post Alignment Table Updates

In Step 4 of Bip-Align, the data obtained from transcript alignment is filtered added to the database. The clone table is updated, and the chromosome, clone_exon and clone_intron tables are updated.

Quality filters:
The followings paramters are available to tune quality filters:

• Minimum percent identity of transcript to genome. Default is 75%
• Minimum number of exons per transcript. Default is 2
• Minimum percent ID of each exon to the genome. Default is 95%
• Max mismatches per exon. If an exon fails the minimum percent ID requirement, then mismatches are counted. This parameter dictates the maximum number of mismatches between the exon and genome. The reason for this extra parameter is to reduce bias against small exons, i.e. a small exon may have a low percent ID to the genome but still have few mismatches.

It is important to note that transcripts which do not pass the set of quality filters do remain in the database, but have no mapping information associated with them. The following tables are updated only if there is a suitable alignment for the transcript.

Table information:

Clone Table	Clone Exon Table
alignment_method	clone_id
chromosome_id	exon_id
orientation	exon_number
chr_beg	chromosome_id
chr_end	orientation
number_exons	clone_beg
percent_id	clone_end
genome_version	clone_sequence
last_updated	chr_beg
	chr_end
	chr_sequence
	percent_id
	mismatches
	splice_junction_5site
	splice_junction_3site
	ss_5end
	map_5end
	ss_3end
	map_3end
	problem_exon

Clone_Intron Table:	Chromosome Table:
clone_id	chromosome_id
intron_id
intron_number
chromosome_id
orientation
position_clone
chr_beg
chr_end
splice_site_5prime
splice_site_3prime

The clone table is the primary table in BIP-Align.
To the chromosome table, there is a many to many relationship. To the CDS table, it is a one to one relationship. To the remaining tables (clone_exon & clone_intron) there is a one to many relationship.

BIP-Align Database Schema

For any comments or suggestions, send an e-mail at: BIP_FEEDBACK@asu.edu