Local Alignment of RNA Sequences with Arbitrary Scoring Schemes Mpi Inf Mpg Form

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once we have checked the quality of our rates and trimmed them if necessary they are ready to proceed to aligning the rates to the reference genome here the goal is to find out from which location the ribs originated from but there are a couple of challenges so our rates opposed to contain genomic variants and they can also contain sequencing errors on the other hand genomes have non unique sequence and introns while our rates come from mature RNA where the introns have been spliced away so the rnaseq aligner needs to be able to map those splice junctions spanning reads to genome non continuously and this is difficult because well while they are splice signals they are relatively weak and on the other hand introns can be thousands of bases long so in this image here we have a piece of genome piece of gene with three exons exon 1 2 & 3 and then we have different kinds of RNA secrets so the red red here maps within an exon and that's easy for the aligner then we have other reads which ac