User: traviata

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Posts by traviata

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Why do PFAM alignments contain 'X'?
... I'm working with the PFAM family [RNA_pol_Rpb2_1 (PF04563)][1]. I've discovered that some of the sequences in the full alignment I downloaded, including `>G1N5G7_MELGA/1-331`, contain the character `X` even though `X` is not a valid protein character. Why is this? Is it related to some sequences ...
pfam written 6 months ago by traviata0 • updated 6 months ago by mbens100
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Can an inter-residue coevolution method be used to detect inter-protein coevolution
... I know like to determine which specific positions in two coevolving proteins are coevolving. One can already determine which positions within a protein are coevolving through methods such as [mutual information][1]. If I wanted to extend this to positions within two protein families instead of just ...
coevolution written 7 months ago by traviata0 • updated 7 months ago by Asaf4.8k
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Answer: A: Output FASTA from Biopython blast result
... I believe I found a solution to my own question. The easiest way to do this seems to through SearchIO instead of NCBIXML. Here is the code I ended up using: from Bio.Blast import NCBIWWW from Bio import SearchIO from Bio import SeqIO base_dir = "/Users/kjsdhjasv/Documents/cs2017/co ...
written 7 months ago by traviata0
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Output FASTA from Biopython blast result
... I'm trying to use the Biopython wrapper for blastp to download matching protein sequences for some sequences that I have stored on my computer. I would like these matching sequences in FASTA format, similar to how on the web server one can select all sequences producing significant alignment and dow ...
fasta biopython blastp bio.blast written 7 months ago by traviata0
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How to download all sequences of a list of proteins for a particular organism
... For every organism here [https://www.ncbi.nlm.nih.gov/genome/browse/reference/#][1], I would like to download the protein sequence of all genes whose `/product ` matches "RNA polymerase subunit" or "ribosomal protein" and put all sequences in a single fasta `proteins.fa`. How can I do this using En ...
entrez direct efetch esearch written 9 months ago by traviata0 • updated 8 months ago by Kevin Blighe24k
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Comment: C: efetch error LWP::Protocol::https not installed
... Your solution worked. Thanks so much! ...
written 9 months ago by traviata0
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efetch error LWP::Protocol::https not installed
... I'm trying to use fetch to download a sequence. However, I keep on getting `501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)` even though I have ran `sudo cpan install LWP::Protocol::https` The terminal output is as follows: $ efetch -db nuccore -id AF086833 -f ...
efetch written 9 months ago by traviata0 • updated 9 months ago by Biostar ♦♦ 20
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Forum: Which institutions offer the best undergraduate education in systems biology?
... For the purpose of this question, let's use MIT's definition of systems biology http://csbi.mit.edu/overview/index.html. I realize that systems biology is not a major, so consider the strengths of biology, bioengineering, or other quantitative departments. ...
systems biology undergraduate forum written 10 months ago by traviata0 • updated 12 weeks ago by ethan1234230
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How does samtools mpileup handle multiple .bam inputs?
... With `samtools mpileup` you can use multiple .bam files as inputs. When samtools computes depth, are these files simply concatenated, or is there a special way samtools synthesizes the data from multiple .bam files? The [samtools github faq][1] seemed to have something about this, but I wasn't exac ...
samtools rna-seq written 11 months ago by traviata0

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Scholar 7 months ago, created an answer that has been accepted. For A: Output FASTA from Biopython blast result

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