User: UnivStudent
UnivStudent • 380
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Posts by UnivStudent
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... Yes, I'm more looking for the helix + loop + sheet cartoon. ...
written 8 weeks ago by
UnivStudent • 380
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... Anyone know how to do something like this?
...
written 8 weeks 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 5 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 2.1 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 2.1 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 2.1 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 2.3 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 2.4 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 2.8 years ago by
UnivStudent • 380
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... You can identify putative DNA binding domains (DBDs) using tools like Pfam, InterPro, hmmscan in HMMER. Since your TFs are eukaryotic you can also use the Protein Scan tool in Cis-BP to identify whether these have DBDs and if they have sequence specificities.
...
written 3.2 years ago by
UnivStudent • 380
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11 weeks ago,
created an answer with at least 3 up-votes.
For A: Find transcription factors that bind to inputted nucleotide sequence?
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2.1 years ago,
created an answer with at least 3 up-votes.
For A: How To Do Pathway Analysis For Mirna Regulation
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For Affyid Mapping Without Chip Info
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For How To Get Tss From Wormmart?
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2.9 years ago,
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For A: Transcription Factor Dna-Binding Sites
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3.2 years ago,
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For A: How can I shuffle a set of sequences while preserving the dinucleotide distribut
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For Best Practices For Using Fimo For Motif Scanning
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4.5 years ago,
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For A: Transcription Factor Dna-Binding Sites
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