User: fishgolden

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fishgolden450
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Posts by fishgolden

<prev • 115 results • page 1 of 12 • next >
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Comment: C: Python script for text matching
... You want to change the background color of motifs in a sequence? Replace "color:red" with "background-color:red". If you want to consider overlap, it will very difficult but you can do it with lower() trick. Continue loop until no change is made by "re.sub" and insert and tag between uppercase ...
written 6 weeks ago by fishgolden450
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Comment: C: Python script for text matching
... OK, let's wait detailed explanation by OP... ...
written 6 weeks ago by fishgolden450
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Comment: C: Python script for text matching
... I thought the final goal is "highlight". The code was updated. ...
written 6 weeks ago by fishgolden450
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Answer: A: Python script for text matching
... I will use "re.sub". # biopython from Bio import SeqIO # regex library import re # file with FASTA sequence infile = r"C:\Users\Lenovo\Desktop\fnl\pyth\Promoter Sequence.fasta" # pattern to search for iupac = 'GGCA' print("") for seq_record in ...
written 6 weeks ago by fishgolden450
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Answer: A: Blastn raw illumina reads all-against-all and return only non-hits
... 1.Use -num_threads option with blastn. 2.I think cat unique_read_ids.dat \ | while read line; do sed -n "/${line}/,/>/p" $query \ | sed '$d'; done \ > result.fn scans whole $query file for each ids in unique_read_ids.dat. Thus makeblastdb -in ${query} -dbtype nucl -p ...
written 9 weeks ago by fishgolden450
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Comment: C: I get this error while creating database on BLAST: BLAST Database creation error
... I think you are going to create db files under C:\Program Files\NCBI\blast-2.10.0+\bin\ . The directory is for installed apps and basically you shouldn't touch anything around there (You don't have a permission to create the files). Call makeblastdb from the directory where you usually use. ...
written 3 months ago by fishgolden450
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Comment: C: Is BLAST highly sensitive?
... > I mean there is whole genome and there is my mRNA which is transcribed from a gene and this gene is in the genome so why can't I find any similarities ? I might misunderstand what you are talking but, the genome of *Hypsibius dujardini* looks that is not booked in refseq_genomes db. I think ...
written 4 months ago by fishgolden450
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Comment: C: Is BLAST highly sensitive?
... > So is this totally normal? Yes. Searching similar nucleotide sequences are really difficult because there are only 4 different types of letters in general. Which variants of BLAST did you use? Using tblastx https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch& ...
written 5 months ago by fishgolden450
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Comment: C: Protein of un-clear function
... At first, you have to make sure that the translated amino acid sequence is the same as you expected and then you can perform sensitive search like [hhsuite][1] and [hmmer][2] [1]: https://github.com/soedinglab/hh-suite [2]: http://hmmer.org/ ...
written 7 months ago by fishgolden450
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Comment: C: Protein of un-clear function
... Hmm all blast hits I can see are hypothetical or predicted proteins... It's quite dangerous to proceed without evidence that the gene is really expressed and translated. ...
written 7 months ago by fishgolden450

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Centurion 13 months ago, created 100 posts.
Scholar 14 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 17 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Popular Question 19 months ago, created a question with more than 1,000 views. For (solved) I couldn't reproduce the problem of max_target_seqs
Supporter 21 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Scholar 23 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction
Student 24 months ago, asked a question with at least 3 up-votes. For (solved) I couldn't reproduce the problem of max_target_seqs
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Scholar 3.4 years ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction

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