User: traviata

gravatar for traviata
traviata0
Reputation:
0
Status:
New User
Last seen:
9 months, 1 week ago
Joined:
1 year, 2 months ago
Email:
w****************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by traviata

<prev • 9 results • page 1 of 1 • next >
2
votes
1
answer
305
views
1
answer
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 9 months ago by traviata0 • updated 9 months ago by mbens100
1
vote
1
answer
342
views
1
answer
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 10 months ago by traviata0 • updated 10 months ago by Asaf4.9k
1
vote
1
answer
756
views
1
answers
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 10 months ago by traviata0
1
vote
1
answer
756
views
1
answer
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 10 months ago by traviata0
6
votes
1
answer
622
views
1
answer
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 11 months ago by traviata0 • updated 11 months ago by Kevin Blighe30k
0
votes
2
answers
1.2k
views
2
answers
Comment: C: efetch error LWP::Protocol::https not installed
... Your solution worked. Thanks so much! ...
written 12 months ago by traviata0
3
votes
2
answers
1.2k
views
5 follow
2
answers
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 12 months ago by traviata0 • updated 26 days ago by Jinguo0
0
votes
0
answers
477
views
0
answers
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 13 months ago by traviata0 • updated 5 months ago by ethan1234230
0
votes
0
answers
905
views
0
answers
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 14 months ago by traviata0

Latest awards to traviata

Scholar 10 months ago, created an answer that has been accepted. For A: Output FASTA from Biopython blast result

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1848 users visited in the last hour