Re: CS 2417 Assignment 1, Q1B

[Michael Brudno]

> Hi Professor Brudno,
>
> For question 1b, how are we to interpret "number of contigs"? For example...
>
>
>  READ#1READ#1READ#1
>                    READ#2READ#2READ#2READ#2READ#2
> DNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNADNA
>
> Would this be 1 contig or 2? If it's 1 contig, then the question is asking
> how many gaps of unsequenced nucleotides exist, but if we're to treat that
> as 2 contigs, then the question becomes much more complicated and requires
> us to calculate the number of reads that have no overlap with other reads
> (relatively easy) and the number of reads that entirely overlap within other
> reads. That latter question becomes, I believe, extremely difficult to
> compute...

The question basically asks if 2 reads that are 1bp away (i.e. have ho
overlap) would be considered to form one or two contigs. You may
consider whichever case you prefer for this.

-Mike

[Aziz Mezlini]

Hi everyone Is there someone still looking for a partner? I am an exchange student from France: Grenoble school of informatics and applied maths(ENSIMAG). I have some biology background too. If you are free, let s agree on a date to discuss project ideas. Aziz --- En date de : Lun 18.10.10, Michael Brudno <bru...@gmail.com> a écrit :