User: lumal29

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lumal2980
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Montreal
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Posts by lumal29

<prev • 13 results • page 1 of 2 • next >
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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 8 days ago by lumal2980
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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 17 days ago by lumal2980
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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 18 days ago by lumal2980
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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 27 days ago by lumal2980
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Comment: C: How to remove duplicated sequences without using any software
... It's weird, maybe try the option "-n" instead of "-s", it removes the sequences by duplicate names instead of duplicate sequences. ...
written 27 days ago by lumal2980
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Answer: A: How to remove duplicated sequences without using any software
... I think Seqkit can make this for you: seqkit rmdup -s your_file.fa -o your_output_file.fa ...
written 27 days ago by lumal2980
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Comment: C: pathway genes for mouse
... I never tried myself, but know it exists, you have this website : [http://geneontology.org/][1]. In case you don't know, Gene Ontology (GO) provides an ontology of defined terms representing gene product properties and it covers three domains: cellular component, molecular function and biological pr ...
written 6 weeks ago by lumal2980
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Answer: A: How to make blast+ 2.2.26 works in a Mac?
... Do you specifically need this version? If so, you can find the link to download it [here][1]. It seems there is a version for Mac. But you can also download the latest version 2.10.0 [here][2]. What you need to do is to unzip it and then use a terminal to use the tools in the "bin" folder inside t ...
written 8 weeks ago by lumal2980
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Comment: C: Residues in contact with ligands in PDB files
... Thank you very much! I heard about Ligplot before, but it's not what I was looking for, as I have to find the residues programaticaly for a several hundreds of pdb files. I would have a question though: If I understand correctly, the residues with a green dash line are supposed to be in contact with ...
written 11 weeks ago by lumal2980
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Comment: C: Residues in contact with ligands in PDB files
... Thank you very much! I don't know Julia very much, just learned the basics, but I will take a look at it, BioJulia looks pretty interesting! I have few questions though: - I guess in the if statement, you select the chain A and the residue 360 which in fact is FMN ligand, but how do you know it's ...
written 11 weeks ago by lumal2980

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Teacher 27 days ago, created an answer with at least 3 up-votes. For A: How to remove duplicated sequences without using any software

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