User: lumal29

gravatar for lumal29
lumal2980
Reputation:
80
Status:
Trusted
Location:
Montreal
Last seen:
4 days, 17 hours ago
Joined:
1 year, 3 months ago
Email:
l************@live.fr

Posts by lumal29

<prev • 19 results • page 1 of 2 • next >
0
votes
1
answer
156
views
1
answers
Comment: C: Check programmaticaly if a protein is mitochondrial with annotations
... Thank you Mensur for your answer. I already used 3 tools to predict the sequences. I used TargetP, Mitofates and PredSL. It's really hard to make a decision based on the results you get from these tools because they don't give the same results. If I look a positive prediction from the 3 tools togeth ...
written 7 weeks ago by lumal2980
0
votes
1
answer
156
views
1
answers
Comment: C: Check programmaticaly if a protein is mitochondrial with annotations
... Hi Antonio, Thank you for your advice! I actually did what you suggest, but with an organism closer in the evolution tree, called Andalucia. I took the proteins that I was sure was mitochondrial, made a database with Blast and use my proteins against it. By doing this, I found proteins like the one ...
written 7 weeks ago by lumal2980
2
votes
1
answer
156
views
1
answer
Check programmaticaly if a protein is mitochondrial with annotations
... Hi, I have a fasta file with more than 38000 protein sequences infered from a genome of Diplonema. All sequences have an ID and an annotation, but the ID is not referenced in any database. I need to check which protein is mitochondrial with the annotations. Here is an example, with an ID and an ann ...
proteomics go terms annotations written 7 weeks ago by lumal2980 • updated 7 weeks ago by Mensur Dlakic6.7k
0
votes
0
answers
128
views
0
answers
Comment: C: Pymol selected residue have dots that are not part of the residue
... Indeed, the representation doesn't affect the distance. ...
written 3 months ago by lumal2980
0
votes
0
answers
128
views
0
answers
Comment: C: Pymol selected residue have dots that are not part of the residue
... Hi, when you select a residue, it selects the atoms of the residues. If you change the representation for sticks for example, you will have a better view of the residue structure with their atoms. ...
written 3 months ago by lumal2980
0
votes
0
answers
181
views
0
answers
Comment: C: Read fasta file
... First, what do you mean by "mobile", what type of device are you talking about? I am not sure what you mean by accessing the fasta file, I would need more details. Regarding the library, if you are familiar with python (and you work on Windows, Mac or Linux), you can use the Biopython library with ...
written 3 months ago by lumal2980
0
votes
1
answer
265
views
1
answers
Answer: A: Biopython vs Python
... Hi, Biopython is a bioinformatics package for python, so you will need to install it with `pip install biopython` in a command line. ...
written 4 months ago by lumal2980
0
votes
1
answer
330
views
1
answers
Comment: C: BLAST Database error: No alias or index file found for nucleotide database [nr]
... to create a database from a fasta file, you can use [BLAST+][1] and you need to use the command makeblastdb Here is the [link][2] for explanations. [1]: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ [2]: https://www.ncbi.nlm.nih.gov/books/NBK279688/ ...
written 4 months ago by lumal2980
1
vote
0
answers
177
views
0
answers
Comment: C: Biopython pairwise sequence comparison using IUPAC?
... The answer to your question is not that trivial, because we can't say the two sequences are "equal", but rather "compatible". For example: ACT and ACA -> False ACT and ACN -> True ACY and ACN -> True ACY and ACR -> False ACY and ACM -> Maybe I don't know the for ...
written 4 months ago by lumal2980
0
votes
2
answers
96
views
2
answers
Comment: C: How to remove duplicated sequences without using any software
... You should read the answer of Mensur Dlakic, because he may be right. Maybe you have different sequences but with the same name, so you should rename the sequences as Mensur suggested to avoid getting rid of sequences that can be useful. ...
written 4 months ago by lumal2980

Latest awards to lumal29

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to remove duplicated sequences without using any software

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1692 users visited in the last hour