User: Anima Mundi

gravatar for Anima Mundi
Anima Mundi2.4k
Reputation:
2,410
Status:
Trusted
Location:
Italy
Last seen:
2 days, 18 hours ago
Joined:
8 years, 4 months ago
Email:
p***************@alice.it

Posts by Anima Mundi

<prev • 320 results • page 1 of 32 • next >
0
votes
0
answers
194
views
0
answers
GenBank entry with apparently unmarked changes
... Dears, I have an mRNA sequence stored as a local file. I retrieved it from GenBank in late 2016 (ID: XM_014915109.1). I just found out that the sequence now appears to be different, but apparently nothing in its GenBank page notifies there were changes after 2016. While it is of course possible tha ...
genbank version update entry item written 5 months ago by Anima Mundi2.4k
0
votes
2
answers
494
views
2
answers
Answer: A: Conversion of full gene description to gene symbols
... Hello, in your shoes I probably would: a) [retrieve all NCBI sequences for your *taxon*][1] in GenBank format b) search for each gene description in your GenBank database (e.g. in the "Official Full Name" field) c) fetch the corresponding gene symbol (i.e. in the "Official Symbol" field) Hope th ...
written 7 months ago by Anima Mundi2.4k
1
vote
4
answers
323
views
4
answers
Answer: A: How to reformat (i.e. to clean) NCBI .fasta archives into a singleline .fasta wi
... A Python 2.7 solution: import sys header = '' seq = '' j = 0 for line in open(sys.argv[1]): j += 1 n = 0 for line in open(sys.argv[1]): n += 1 if line[0] == '>': print seq seq = '' for char in ...
written 8 months ago by Anima Mundi2.4k
0
votes
3
answers
4.3k
views
3
answers
Comment: C: Locating A Sequence In A Fasta File.
... Hi jleandroj, When asked to enter the subject, you should copy-paste the genome sequence from its FASTA (or whatever sequence you want to parse for occurrences of the first one). Please just note that, as it is, the script is case-sensitive and does not allow newlines. Hope this helps. ...
written 8 months ago by Anima Mundi2.4k
0
votes
1
answer
412
views
1
answers
Comment: C: Find all sequence of a specific genus amplified by a couple of primers
... Assuming you performed your PCR on cDNA, checking for amplicons from genome is merely a way to check for potential sources of genomic contamination. Doing this using your whole amplicon would just return genomic locations in which your full amplicon (or something thereof) is present, if any. For ins ...
written 11 months ago by Anima Mundi2.4k
0
votes
1
answer
412
views
1
answers
Answer: A: Find all sequence of a specific genus amplified by a couple of primers
... Hello, a rapid way to do that is to: 1) reverse-complement (RC) your right primer 2) build your subject database as a FASTA file (if needed) 3) go to [NCBI nucleotide BLAST][1] 4) paste your left primer, type a series of Ns right next to it, then paste your RC right primer 5) load your databas ...
written 11 months ago by Anima Mundi2.4k
0
votes
2
answers
599
views
2
answers
Comment: C: transition to bioinformatics
... Hi, just a quick comment. > But I really want this, I really like it. Just roll with it ;) Nowadays there is a strong need for bioinformaticians, if you happen to have a strong interest for bioinformatics and you are fresh from a degree in biology then you are in luck, in my opinion. ...
written 12 months ago by Anima Mundi2.4k
0
votes
1
answer
318
views
1
answers
Comment: C: Change nexus textlabels
... Yep, indeed the script was simply meant to help you re-format your list IDs, as you originally requested. If you want to get some help then... you should help people to help you! For instance, in the original question at least you were pointing out to one example ID. That said, unfortunately I am no ...
written 12 months ago by Anima Mundi2.4k
1
vote
1
answer
318
views
1
answers
Comment: C: Change nexus textlabels
... Well, this was meant to reply to an original question, now missing -.-'' ...
written 12 months ago by Anima Mundi2.4k
0
votes
1
answer
318
views
1
answers
Answer: A: Change nexus textlabels
... Hi, if you want to try replacing headers, this should do the job (Python 2.7 script, takes the two list filenames as arguments): import sys listA = [] listB = [] for line in open(sys.argv[1]): listA.append(line.replace('\n','')) for line in open(sys.argv[2 ...
written 12 months ago by Anima Mundi2.4k

Latest awards to Anima Mundi

Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Is A Gap At The Same Position In Query And Template Possible?
Great Question 12 weeks ago, created a question with more than 5,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Great Question 3 months ago, created a question with more than 5,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Student 3 months ago, asked a question with at least 3 up-votes. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 5 months ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Popular Question 6 months ago, created a question with more than 1,000 views. For NCBI is going to eliminate GI identifiers
Popular Question 9 months ago, created a question with more than 1,000 views. For Transcriptome Microarray Database
Popular Question 10 months ago, created a question with more than 1,000 views. For Transcriptome Microarray Database
Epic Question 10 months ago, created a question with more than 10,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Epic Question 10 months ago, created a question with more than 10,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 11 months ago, created a question with more than 1,000 views. For How To Download All The Introns From Ensembl
Scholar 13 months ago, created an answer that has been accepted. For A: Retrieving RNA sequence from corresponding genomic coordinates
Great Question 15 months ago, created a question with more than 5,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 15 months ago, created a question with more than 1,000 views. For Meme-Suite Is Down... Does Anybody Know What'S Happening?
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Great Question 16 months ago, created a question with more than 5,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Should Fasta Be Capitalized?
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Is A Gap At The Same Position In Query And Template Possible?
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Use Bedtools To Extract Promoters From A Mouse Bed File
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Display Old Assemblies Of The Mouse Genome In The Ensembl Genome Browser
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Is A Gap At The Same Position In Query And Template Possible?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 952 users visited in the last hour