User: UnivStudent

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UnivStudent360
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Posts by UnivStudent

<prev • 44 results • page 1 of 5 • next >
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How do you plot secondary structure like PDB?
... 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? ...
pdb plot secondary strucure ribbon draw written 9 days ago by UnivStudent360 • updated 9 days ago by jrj.healey4.2k
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Answer: A: Find transcription factors that bind to inputted nucleotide sequence?
... 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 UnivStudent360
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Comment: C: Aligning Copies Of A Protein Domain To A Pfam Model (HMM)
... 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 UnivStudent360
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Aligning Copies Of A Protein Domain To A Pfam Model (HMM)
... 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 ...
alignment sequence hmm clustal omega pfam written 20 months ago by UnivStudent360
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Answer: A: Download transfac public database
... 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 UnivStudent360
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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 UnivStudent360
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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 UnivStudent360
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Answer: A: Prediction Transcription Factor Families
... 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 UnivStudent360
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Answer: A: Transcription Factor (TF) sequence extraction +/- 2000 of Arabidopsis thaliana
... 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 UnivStudent360
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Comment: C: Automatic Data Extraction From Timetree
... 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 UnivStudent360

Latest awards to UnivStudent

Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How To Do Pathway Analysis For Mirna Regulation
Popular Question 21 months ago, created a question with more than 1,000 views. For Affyid Mapping Without Chip Info
Popular Question 22 months ago, created a question with more than 1,000 views. For How To Get Tss From Wormmart?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Transcription Factor Dna-Binding Sites
Scholar 2.8 years ago, created an answer that has been accepted. For A: How can I shuffle a set of sequences while preserving the dinucleotide distribut
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Best Practices For Using Fimo For Motif Scanning
Supporter 4.1 years ago, voted at least 25 times.
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Transcription Factor Dna-Binding Sites

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