User: dabid

gravatar for dabid
dabid0
Reputation:
0
Status:
New User
Last seen:
1 week, 3 days ago
Joined:
4 months, 4 weeks ago
Email:
d****@vt.edu

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

This helps us discourage the inappropriate use of our site.

Posts by dabid

<prev • 17 results • page 1 of 2 • next >
0
votes
1
answer
275
views
1
answers
Comment: C: Any tool that aligns sequences that use degenerated nucleotide coding
... It's primer sequences and I need to align them to some database.. Thank you for your suggestions, I will look at them closely and see it works for my case ...
written 12 weeks ago by dabid0
0
votes
1
answer
275
views
1
answers
Comment: C: Any tool that aligns sequences that use degenerated nucleotide coding
... Thank you Jean, it's really good point to process these sequences one by one on the fly. But still, to run blast, I need to write these sequences into a file. **NcbiblastnCommandline** doesn't support a list or generator object. I am not sure how much multi-threading or parallel processing is going ...
written 12 weeks ago by dabid0
0
votes
1
answer
275
views
1
answers
Comment: C: Any tool that aligns sequences that use degenerated nucleotide coding
... Can you please explain to me what do you mean by handle degenerated bases on the reference. Can it consider these degenerated bases in the alignment as matches and not as mismatches -all the time? ...
written 12 weeks ago by dabid0
0
votes
1
answer
275
views
1
answers
Comment: C: Any tool that aligns sequences that use degenerated nucleotide coding
... unfolding all the ambiguous sequences is impossible: a file of few ko can turn on to a file of more than 400 GO (I tried to do that, then I gave up as my disk of 500 GO run out of space..). I thought about implementing my own tool, but wanted to check if there is any existing tool first. For the reg ...
written 3 months ago by dabid0
0
votes
1
answer
275
views
1
answers
Comment: C: Any tool that aligns sequences that use degenerated nucleotide coding
... Yeah, I got that from the beginning, I need a tool that doesn't consider the degenerated nucleotide coding as a mismatch unless it's actually for a mismatch. For example, N should never be a mismatch, however R matches with A and G, and mismatches with T and C. Any suggestions? ...
written 3 months ago by dabid0
0
votes
1
answer
275
views
1
answers
Comment: C: Any tool that aligns sequences that use degenerated nucleotide coding
... I am not sure if I can share my files here in this platform. I can email it to you if you want.. But, anyway, I am sharing a case of the blastn results below: GCCT**NA**GGC GCCT**CT**GGC with "align_len": 9 and "identity": 7 which shouldn't be the case, the identity should be 8 as N can be any nuc ...
written 3 months ago by dabid0
0
votes
1
answer
275
views
1
answers
Comment: C: Any tool that aligns sequences that use degenerated nucleotide coding
... I have tried Blastn, but it doesn't understand IUPAC codes unless there is some option that I need to set up and I am not aware of it.. Please, let me know.. For exonerate, I am not aware of it, I will have a look at it shortly. ...
written 3 months ago by dabid0
1
vote
1
answer
275
views
1
answer
Any tool that aligns sequences that use degenerated nucleotide coding
... Hi, I have short sequences that use degenerated nucleotide coding (such R, Y B, N, etc). I want to align these sequences to another longer sequence that uses only standard nucleotide (A, T, C , and G). As an example, the tool should align N to either A or T or C or G. So, it doesn't consider N as a ...
alignment sequence degenerated coding dna written 3 months ago by dabid0 • updated 3 months ago by Jean-Karim Heriche13k
1
vote
1
answer
186
views
1
answers
Answer: A: prophage database to generated simulated prophage reads
... I found this database, it seems that it hasn't been updated since 2010, but it's a good start.. http://aclame.ulb.ac.be/Tools/Prophinder/ ...
written 3 months ago by dabid0
1
vote
1
answer
269
views
1
answers
Answer: A: get gene annotation for nucleotide sequence of the NCBI RefSeq database
... Maybe it is not an exact answer for my question, but as a turn around, what I needed doing is downloading the bacteria genomes that I need from the NCBI RefSeq database as a genbank files. Then, it's easy to process these genbank files using Biopython library to get CDs, etc. ...
written 3 months ago by dabid0

Latest awards to dabid

Scholar 3 months ago, created an answer that has been accepted. For A: prophage database to generated simulated prophage reads
Scholar 3 months ago, created an answer that has been accepted. For A: get gene annotation for nucleotide sequence of the NCBI RefSeq database

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1373 users visited in the last hour