User: UnivStudent
UnivStudent • 380
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Posts by UnivStudent
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... I've also used [PWMclus][1] in "CCAT: Combinatorial Code Analysis Tool for transcriptional regulation." for a task like this with good results. I will warn that this type of analysis wouldn't work well for many families (especially Zinc Fingers) with very diverse motifs if you choose a single consen ...
written 17 months ago by
UnivStudent • 380
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... Yes, I'm more looking for the helix + loop + sheet cartoon. ...
written 20 months ago by
UnivStudent • 380
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... Anyone know how to do something like this?
...
written 20 months ago by
UnivStudent • 380
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... Does anyone know the software PDB uses to draw the chain's secondary structure (DSSP line)? Or any other programs that can draw the same type of diagrams programatically?
...
written 23 months ago by
UnivStudent • 380
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... I'd recommend the ["Scan single sequences for TF binding"][1] tool in CIS-BP using TFs from whatever species you're interested in, or TFs that you're interested in and added to your cart. Alternatively, [FIMO][2] is a popular tool from the MEME suite that can be used online, or run on the command li ...
written 3.5 years ago by
UnivStudent • 380
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... It looks like instead of the HMM you'd have to input the seed alignment used to create the HMM, but it's worth a shot.
UPDATE: This method does not scale well, and can't be used with large numbers of sequences (~60k) even with multiple cores and lots of memory. ...
written 3.5 years ago by
UnivStudent • 380
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... I'm wondering if anyone out there has any experience aligning copies of a protein domain to it's Pfam domain using the HMM. Currently I'm aligning large numbers (1 - 100k) of sequences with [Clustal Omega][1] and supplying the Pfam using the `--hmm-in` parameter to guide the alignment, however I'm u ...
written 3.5 years ago by
UnivStudent • 380
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... You can download the Transfac public matrices and much more in the [CIS-BP][1] database. Just select Transfac from the evidence type dropdown.
[1]: http://cisbp.ccbr.utoronto.ca/ ...
written 3.8 years ago by
UnivStudent • 380
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Answer:
A: Motifs data base
... If they're RNA motifs try the motif scan in [CIS-BP-RNA][1] to find related motifs from RNA-binding proteins using Tomtom. If they're DNA try the motif scan in [CIS-BP][2] to find related motifs from TFs using Tomtom.
[1]: http://cisbp-rna.ccbr.utoronto.ca/TFTools.php
[2]: http://cisbp.ccbr.u ...
written 3.9 years ago by
UnivStudent • 380
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Answer:
A: htseq-count cannot find pysam
... I had a similar problem using the latest version of pysam and HTSeq. I had to go back a version, and use https://pypi.python.org/pypi/pysam/0.8.3 to get it to work again. ...
written 4.3 years ago by
UnivStudent • 380
• updated
3 months ago by
RamRS ♦ 26k
Latest awards to UnivStudent
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: Find transcription factors that bind to inputted nucleotide sequence?
Teacher
3.5 years ago,
created an answer with at least 3 up-votes.
For A: How To Do Pathway Analysis For Mirna Regulation
Popular Question
3.7 years ago,
created a question with more than 1,000 views.
For Affyid Mapping Without Chip Info
Popular Question
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For How To Get Tss From Wormmart?
Teacher
4.4 years ago,
created an answer with at least 3 up-votes.
For A: Transcription Factor Dna-Binding Sites
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4.6 years ago,
created an answer that has been accepted.
For A: How can I shuffle a set of sequences while preserving the dinucleotide distribut
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4.7 years ago,
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For Best Practices For Using Fimo For Motif Scanning
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For A: Transcription Factor Dna-Binding Sites
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