User: Dhillonv10

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Dhillonv10100
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Posts by Dhillonv10

<prev • 13 results • page 1 of 2 • next >
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Obtaining Downstream Non-Coding Sequences For A Gene From Ucsc Or Ensembl
... Background: In this study [1] "Transposable elements have rewired the core regulatory network of human embryonic stem cells" the authors mention that they obtained 20kb of both upstream and downstream non-coding sequences for certain genes. Question: To keep this brief, let's generalize this to sa ...
ensembl ucsc written 7.0 years ago by Dhillonv10100 • updated 7.0 years ago by Emily_Ensembl20k
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Firepro For Linear Motifs From Elm Database
... Hi all, Has anyone here used FirePro motif finder? If so, can anyone show me an example of where one can take a sequence of multiple instances of one motif from ELM database and convert it to the data that FirePro needs? Firepro requires data so that: The data input to FIRE-pro is a "protei ...
software motif written 8.1 years ago by Dhillonv10100
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Comment: C: Scoring The Results From Different Motif Discovery Software
... thanks @cabbagesofdoom, the slimcheck function is definitely something to look at, see I got the following results, SlimFinder: S..K.TQT now another tool DiLiMOT gives me: KxTQT I'm just looking for a way to compare these two results, this was only for one motif, now if I can come up with a generali ...
written 8.2 years ago by Dhillonv10100
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Comment: C: Scoring The Results From Different Motif Discovery Software
... thanks for your answer Larry, I've been thinking of simply adding scores and such but how would one answer this using your approach, I got this pattern from SlimFinder: S..K.TQT now another tool DiLiMOT gives me: KxTQT now how does one score this? ...
written 8.2 years ago by Dhillonv10100
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Fire-Pro Gene Expression Profile
... I'm trying to use Fire-pro to find motifs in linear motifs taken from ELM database. However, using the software, the syntax comes as follows: perl $FIREPRODIR/fire_aa_wrapper.pl --expfile=<inp> --exptype=<type> --species=<sp> --runname=<dir/prefix> where inp indicates th ...
software perl motif written 8.2 years ago by Dhillonv10100
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Comment: C: Scoring The Results From Different Motif Discovery Software
... thanks for your answer @maximilianh, TAMO is unfortunately another DNA-sequence motif discovery method, I'm working with protein-motifs such as the ones from ELM database. ...
written 8.2 years ago by Dhillonv10100
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Scoring The Results From Different Motif Discovery Software
... Hi all, I'm trying to compare the results from different protein motif discovery tools out there such as FirePro, Slimfinder and MEME. So after running the same data through each of hte softwares, I get some nice results now then the question becomes which software did better? Note that there 3 fin ...
motif scoring algorithm written 8.2 years ago by Dhillonv10100 • updated 6.0 years ago by Biostar ♦♦ 20
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Comment: C: Most Frequent Nucleotide/String Pattern In Dna Sequence Files Using Python Or Bi
... yup it worked as needed. ...
written 8.2 years ago by Dhillonv10100
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Comment: C: Most Frequent Nucleotide/String Pattern In Dna Sequence Files Using Python Or Bi
... @brentp, it turns out if you cast a string at seq_record.seq, it works out perfectly. So if you could edit your answer here: seq = (str) seq_record.seq ...
written 8.2 years ago by Dhillonv10100
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Comment: C: Most Frequent Nucleotide/String Pattern In Dna Sequence Files Using Python Or Bi
... @DK: you ROCK!!!! thanks a lot, wow i've been trying to work this out for a long time and it finally worked out. ...
written 8.2 years ago by Dhillonv10100

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