User: Mensur Dlakic

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Mensur Dlakic8.1k
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http://www.montana.edu...
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1 year, 6 months ago
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Posts by Mensur Dlakic

<prev • 811 results • page 1 of 82 • next >
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Answer: A: Why are there soo many hits when using KOFAMSCAN?
... ATP-binding transporters are one of the largest and most promiscuous protein superfamilies - see [**here**][1]. Their overall structure is the same and is different mostly in parts that bind and recognize the substrate. That is a relatively small portion of the protein, so most if not all transporte ...
written 12 hours ago by Mensur Dlakic8.1k
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Comment: C: Unable to find this E coli genome
... cDNA file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/GCA_000800765.1_ASM80076v1_cds_from_genomic.fna.gz Click on `FTP directory for GenBank assembly` ...
written 12 hours ago by Mensur Dlakic8.1k
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Answer: A: Unable to find this E coli genome
... Here is the description: https://www.ncbi.nlm.nih.gov/assembly/GCF_000800765.1/ Full directory: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/ Genomic DNA: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/GCA_000800765.1_A ...
written 17 hours ago by Mensur Dlakic8.1k
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Answer: A: Generate random DNA sequences with variable %identity based on a reference seque
... This short python script will read a fasta file and randomly mutate the requested fraction of nucleotides. Save it as `mutate_dna.py` and run: python mutate_dna.py dna.fa 0.2 > mutated_dna.fa You will need to run it multiple times with different mutation rates to get what you want. Startin ...
written 19 hours ago by Mensur Dlakic8.1k
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Answer: A: Can you tell whether the cell was dead or not using RNA-seq data?
... If you are asking whether there is some kind of RNA signal that is present in live vs. dead cells (or *vice versa*), the answer is probably no. RNA is short-lived even in live cells, but it is constantly made and there is always a good amount of it present. I don't think there would be much differe ...
written 23 hours ago by Mensur Dlakic8.1k
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Comment: C: What is the best way to assemble Illumina paired end reads?
... Given the (lack of) information you have given us, it is the same as if you asked what is the best way to measure the square footage of a room. There are so many way to accomplish such a non-descript task that you will not be getting meaningful suggestions to your problem, but rather individual pref ...
written 2 days ago by Mensur Dlakic8.1k
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Comment: C: Making a custom Transcriptome
... From what I remember when using `kallisto` last time, the reference transcriptome is a simple FASTA file with multiple sequences. If so, that would be a text file to which you can add your own sequence(s) using any editor. ...
written 3 days ago by Mensur Dlakic8.1k
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Answer: A: Building a phylogenetic tree based on some selected strains of bacteria sequence
... For genomes of this size it makes little sense to align them whole. Not only is that impractical (time-consuming, and it may require very large memory), but it is not very informative in terms of biology because of codon degeneracy. It is possible to have two genomes that are 70% identical at nucleo ...
written 5 days ago by Mensur Dlakic8.1k
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Comment: C: hmmindex: FATAL: failed to open HMM file Pfam-A.hmm for reading.
... The file you downloaded contains sequences. You probably want the file with HMMs. http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz After gunziping the file, find the exact accession numbers: grep PF00115 Pfam-A.hmm `ACC PF00115.21` grep PF07714 Pfam-A.hmm `ACC PF ...
written 6 days ago by Mensur Dlakic8.1k
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Answer: A: Confused about sequence motif regular expressions
... Regular expressions in this case represent sequences, not individuals. If the sequences that were used to build this expression came from a single individual, it will refer to that individual. For practical purposes, short expressions such as the one you are using are guaranteed to occur multiple ti ...
written 10 days ago by Mensur Dlakic8.1k

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Teacher 19 hours ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 19 hours ago, created an answer that has been accepted. For A: Prottest output to Raxml input
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Scholar 13 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Appreciated 16 days ago, created a post with more than 5 votes. For A: Multiple alignment software
Teacher 16 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Appreciated 29 days ago, created a post with more than 5 votes. For A: Multiple alignment software
Teacher 29 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 5 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
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