Exercise 4 : Gene prediction

Objective: identify gene in human genomic sequences

We will use three different approaches to identify genes within a human  genomic sequence . Compare the results of each method.

First of all, it is necesary to identify and mask repeated sequences:

• RepeatMasker ( ***    *** )

1- Methods ab initio

• Grail ( ***   *** )
• Genscan ( ***  *** )

2- Search for transcribed regions (EST, cDNA) in genomic DNA

• Search for ESTs matching the genomic sequence (masked): BLAST (NCBI)  (use database est_human) ( *** )
• Copy the first 20 ESTs, and retrieve sequences from NCBI BLAST output  at PBIL  ( *** )
• Assemble ESTs with CAP3  ( ***    *** ) (save Assembly in a text file)
• align the cDNAs and genomic DNA with  SIM4 ( ***    ***   *** )

 

3- Comparative approach: search protein coding regions by similarity

• Search for proteins matching the genomic sequence (masked) with BLASTX (translated BLAST searches): BLAST (NCBI)(use database swissprot)( *** )
• Retrieve the closest homologue ( *** )
• Alignment this protein to the genomic DNA with  GENEWISE (Pasteur) (parameter: genewise protein to genomic DNA)( *** )

5- Now repeat the same exercise with two other human genomic sequences:  genomic1   genomic2