Storing And Manipulating Net Alignments Using Bioconductor

Question

[Nathan Harmston]

Hi,

I'm currently working with the net alignments available from the UCSC. I was hoping that there would be a bioconductor package out there that would allow me to both store this data and manipulate it - but a look around hasn't really turned anything up. I was wondering if I've missed something during my searches or what people use to manipulate this type of data programmatically (in R or anything else). I'd ideally want to be able to handle alignments between synteny blocks in multiple species - not just pairwise. Thanks

[Martin Morgan]

rtracklayer::liftOver ?

[Nathan Harmston]

not really what I was looking for - I'm going to just write my own parser - store it in a database and pump it into GRanges. I was really looking to play with the net alignments not the chain files - which seems to be all thats possible with rtracklayer