Hi, I was hoping someone could help with this. I am trying to find long runs of trinucleotide repeats, and only those in exons of genes. I already did a run-through with Tandem Repeat FInder, and now I want to try with Repeat Masker (both through the tables function of Genome Browser). My issue is narrowing the results down to what I need and that I can work with. I am using the latest Cow Genome assembly, I have created an intersection with RefSeq Genes. I have also only chosen Simple repeats and Low Complexity repeats. The repeats themselves do not have to be perfect, as long as they encode the same amino acid, so a mixed run of CAA & CAG would be great because they are all Glutamine. My list is absolutely monstrous so if anyone knows if there is a way to narrow it down to show say, only those that are long repeats or poly-amino acids (no di-, hexa, etc -nucletide repeats either).... THANK YOU Amanda
Hi. The files are outputted as "Hyperlinks to Genome Browser", there is only one column with all the repeats one after the other, each linking to the display within genome browser. I then have to go into the display for each hyperlink, and check the predicted protien of the gene for every one, and there are hundreds, including mononucleotides to hexanucleotides, and specific nucleotide rich sequences. I emailed the folks at Genome Browser and they suggested using the Simple Repeat track only, however, this option misses many of the mixed-codon repeats I require. Here is what the output looks like:
(CCG)n at chr11:37850173-37850199
(TCC)n at chr11:37879560-37879586
AT_rich at chr11:37903786-37903822
GC_rich at chr11:39304343-39304380
(CGG)n at chr11:39304422-39304474
(TCC)n at chr11:39304513-39304559
AT_rich at chr11:39481898-39481934
GC_rich at chr11:39720369-39720390
AT_rich at chr11:39750047-39750074
(CGG)n at chr11:39804726-39804759
AT_rich at chr11:39815433-39815476
AT_rich at chr11:39815537-39815560
AT_rich at chr11:44853996-44854036
GC_rich at chr11:44954533-44954571
AT_rich at chr11:45324996-45325023
AT_rich at chr11:45439656-45439677
AT_rich at chr11:47597196-47597216
(TG)n at chr11:47620452-47620505
AT_rich at chr11:48052475-48052509
AT_rich at chr11:48151925-48151953
AT_rich at chr11:48182914-48183002
AT_rich at chr11:48244595-48244622
It would be great to find a way to narrow this down to only what I need... Thanks so much for your response, Amanda
I think you accidentaly put this as an answer instead of editing original question.
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To best help you with this, you will probably have to show an example of the kind of data you are getting. From your question, you have done an intersection between refseq and Simple + Low complexity repeats on UCSC, however, we have no idea what the file output you have looks like. Do one of the columns specify "long repeats"? Could you paste some of your output and highlight it and press the code button so it formats nicely?