Venter genome

[ashkot]

Hi all,
I want to query the Venters genome (HuRef database). The sequencing technology used is the Sanger sequencing method.

Each of the chromosome file is available as .fasta file.

Has anyone ever converted these .fasta files into SAM/ BAM files? Can this be done?

Alternative, what would be a good way to batch query that genome.

Thanks,
Ashwin

[adaptivegenome]

SAM/BAM are alignments. So you would not want to encode an assembled sequenced in this format. If you have a single sequence you can make a blast-able database and query via BLAST.

[mgogol]

What are you querying for? If you're trying to align something to it, fasta is a fine format...

[ashkot]

hi there,
what i really want is genotypes at chromosomal coordinates. Since the data is available in .fasta format for every chromosome, i am looking at a way to generate a list of genotypes accross the entire chromosome and was wondering if the .fasta can be converted to .bam and finally VCF. But it seems not, is there some other way this can be accomplished?