BIP-Align

BIP-Align is the first tool used in the BIP Toolbox pipeline. It can be used alone to create an alignment database, or with other BIP tools to create a database for a more specific function.

Objective:

The objective of BIP-Align is to map input transcripts to a given organism's genome, then store information in a database. Data is subject to user-definable quality filters. The following data is stored:

• Transcript ID
• mRNA/cDNA/EST sequence
• CDS region
• Functional annotation
• Library/tissue information
• Alignment to the genome, including exon/intron structure

This module creates the following entities:

• Chromosome ID
  Identifies the chromosomes with unique IDs. For example, human chromosomes will be identified by chrN where N is the chromosome number. D. melangaster chromosomes are identified by chromosome number and arm.
• Transcript ID
  This is a unique identifier for each mRNA/cDNA/EST sequence processed. There can be many different transcripts mapped to one chromosome.
• Transcript sequence
  This is taken from the input data. There is only one sequence per transcript
• CDS region
  Coding sequence. Each transcript has zero or one. This is provided by the input data, and is not calculated by BIP-Align
• Functional annotation
  This also is provided by the input data. Each transcript will have zero or one
• Library/tissue
  Provided by input data. Each transcript has zero or one
• Alignment to genome
  Each transcript has one alignment to the genome. Transcript alignments failing the quality filters are not stored.
• Exons
  Product of transcript alignment. There are one or more exons per transcript .

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BIP-Align performs the following steps:

1. Obtain transcript and genome data.
     Currently the user must manually download the genome and transcript data.   Wrappers will be developed which automatically fetch data from the following sources:  
   • UCSC (Genome data)
   • GenBank (Full-length mRNAs)
   • dbEST (EST data)
   • UniGene (Transcript data)
     Other data sources can be added by request
   Where and how to download the input data
2. Load data into database. Information is added to the clone and cds tables. Details
3. Align all transcripts to genome   Current design uses a two-step alignment process utilizing Blat, then feeding the output through SIM4 to refine the alignment.
   Details
     Other alignment tools will be added if needed.
4. Store alignment data in database. Alignments have been filtered according to quality in step 3. Here the clone, chromosome, clone_exon and clone_intron tables are updated. Details on quality filter and updated fields.
   BIP-Align Database Schema
   
   For any comments or suggestions, send an e-mail at: BIP_FEEDBACK@asu.edu