User: UnivStudent
UnivStudent • 360
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Posts by UnivStudent
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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 9 days ago by
UnivStudent • 360
• updated
9 days ago by
jrj.healey • 4.2k
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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 20 months ago by
UnivStudent • 360
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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 20 months ago by
UnivStudent • 360
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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 20 months ago by
UnivStudent • 360
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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 23 months ago by
UnivStudent • 360
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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 2.0 years ago by
UnivStudent • 360
2
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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 2.4 years ago by
UnivStudent • 360
0
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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 2.8 years ago by
UnivStudent • 360
0
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757
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... You can find the resource you need using the upstream/downstream sequence tool using TAIR IDs (https://www.arabidopsis.org/tools/bulk/sequences/index.jsp). Same thing using the Phytozome BioMart (which is probably accessible in R)
...
written 2.8 years ago by
UnivStudent • 360
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... Any chance you have or know of a new solution to this problem? Would love to get some of the data off the site.
...
written 2.8 years ago by
UnivStudent • 360
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