Hello everyone,
I'm student in computer science and I work on a bioinformatics project which has to analyze a LastGraph file of Velvet. So I'm not an expert in bioinformatics but I think I know at least the basics to achieve my project. I read the paper about Velvet and the manual.
The problem is now, I have an example of LastGraph file in front of me and I don't understand how it works in relation to the description given in the paper.
In the manual, they say about the nodes :
"This means that the two sequences given above are not reverse-complements of each other but reverse-complements shifted by k nucleotides".
I am not sure to understand that ...
For example, I have in my LastGraph file this node :
I see that the first 91 nucleotides of each sequence here are the reverse-complements of the first 91 nucleotides of the other sequence.
I thought during a while that each sequence given in this node corresponds to some overlapping words of length k, but this would mean that that last k-1 nucleotides of this node overlap exactly on the first k-1 nucleotides of the node connected to this one. Or in my file, this is never the case.
I think there is something important that I did not understand and I would be very grateful if you could explain it to me.
I have another question : in the Velvet manual, they say at the end that there is a tool named "layout" that allow to transform the LastGraph file into DOT file but it is not inside the last version of Velvet ... did they delete it ?
Thank you for you help !
Best
I'm student in computer science and I work on a bioinformatics project which has to analyze a LastGraph file of Velvet. So I'm not an expert in bioinformatics but I think I know at least the basics to achieve my project. I read the paper about Velvet and the manual.
The problem is now, I have an example of LastGraph file in front of me and I don't understand how it works in relation to the description given in the paper.
In the manual, they say about the nodes :
"This means that the two sequences given above are not reverse-complements of each other but reverse-complements shifted by k nucleotides".
I am not sure to understand that ...
For example, I have in my LastGraph file this node :
Code:
NODE 1 161 602 602 0 0 0 0 0 0 ACTAACAGTCCTGTTATATCCCTAGGTCTTTCTAACGCGGGGGCGGCCGTAATTTTGCAATTTACTCCCATTGCTGAGGCTAAAATCAGGGAAATGGTGGTTTTTCCCAGGCCAGGGGGCCCATATAAGAGGAGATGATCCATCGGTTCATTACGGGTTTT CCCTGATTTTAGCCTCAGCAATGGGAGTAAATTGCAAAATTACGGCCGCCCCCGCGTTAGAAAGACCTAGGGATATAACAGGACTGTTAGTTAGCTTAAAACCAGGAGATATTCTATTTATTGATGAAATTCATCGGCTTAACCGTTTAACCGAAGAATTG
I thought during a while that each sequence given in this node corresponds to some overlapping words of length k, but this would mean that that last k-1 nucleotides of this node overlap exactly on the first k-1 nucleotides of the node connected to this one. Or in my file, this is never the case.
I think there is something important that I did not understand and I would be very grateful if you could explain it to me.
I have another question : in the Velvet manual, they say at the end that there is a tool named "layout" that allow to transform the LastGraph file into DOT file but it is not inside the last version of Velvet ... did they delete it ?
Thank you for you help !
Best
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