User: Prohan

gravatar for Prohan
Prohan350
Reputation:
350
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Trusted
Location:
United States
Last seen:
2 years, 8 months ago
Joined:
8 years, 10 months ago
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p*****@gmail.com

Posts by Prohan

<prev • 21 results • page 1 of 3 • next >
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Download all sequences for a KEGG pathway
... Hi, I'm trying to get all the sequences associated with a KEGG pathway. I'm specifically trying to get all the sequences associated with this: ko00910 Thanks ...
gene written 3.0 years ago by Prohan350
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Answer: A: Automated Primer-Blast like funcionnality
... Hi I've found the EMBOSS tool "primersearch" to be the most straightforward - for whatever reason they don't call it an in-silico pcr tool but that's what it does. http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/primersearch.html ...
written 5.1 years ago by Prohan350
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Comment: C: Nucleotide CDS from RefSeq?
... Thanks for the info. I'm trying to do it locally by parsing the genbank files rather than htting the NCBI/embl servers a ton.  ...
written 5.2 years ago by Prohan350
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Nucleotide CDS from RefSeq?
... Hi All, I'm trying to retrieve the nucleotide sequences of the complete RefSeq protein CDS's. I've looked at the files at ftp://ftp.ncbi.nih.gov/refseq/release/complete/ but I can't seem to find a file that has the CDS + the original nucleotide (whole genome) sequence that the CDS came from. I don ...
ncbi biopython genbank written 5.2 years ago by Prohan350 • updated 5.2 years ago by eddie.im130
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Answer: A: Shall We Go Back To Stackexchange?
... Yes - not sure what the real motivation was to move away. ...
written 6.7 years ago by Prohan350
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Comment: C: Reduce Blast Xml Size?
... I've been parsing the human readable blast output just fine without any problems - although it supposedly can change whenever NCBI feels like it. As for the tabbed output - never had a problem with that. I'd prefer XML too but the files are sssoooo big ...
written 7.4 years ago by Prohan350
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Answer: A: Showing Queries With No Hit In Tabbed Blast Output?
... Thanks to Pierre's inspiration I had implemented into a Python script. Eventually though I came up with a bash one-liner: lasthit=$(tail -n 1 input.fasta.blastn | awk '{print $1}') && grep '^> input.fasta | grep -n $lasthit Basically - the last hit of the tab blast output is read by "tai ...
written 7.4 years ago by Prohan350
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Comment: C: 454 Bacterial Genome Annotation
... You can also submit your sequences to the IGS annotation pipeline (basically the TIGR/JCVI pipeline. JGI let's you submit to IMG as well, but they are slower. With those two you basically email them and send them your sequence. So you get more support, but RAST is good for a quick annotation. On an ...
written 7.5 years ago by Prohan350
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Comment: C: Parsing Ncbi Taxonomic Tree?
... This is really impressive bash scripting. It seems to work great for me. Now just need to understand how it works! Thanks a ton. ...
written 7.5 years ago by Prohan350
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Comment: C: Reduce Blast Xml Size?
... The file size isn't so much an issue but the time it takes to iterate through the files that's annoying. The whole reason I'm trying to do this is to get the full description of the hit. My solution now has been to directly parse the human readable default blast out to tab delimited. These are much ...
written 7.5 years ago by Prohan350

Latest awards to Prohan

Prophet 3.2 years ago, created a post with more than 20 followers. For Parsing Ncbi Taxonomic Tree?
Great Question 5.0 years ago, created a question with more than 5,000 views. For Parsing Ncbi Taxonomic Tree?
Epic Question 5.0 years ago, created a question with more than 10,000 views. For Parsing Ncbi Taxonomic Tree?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Newbler And Ubuntu?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Reduce Blast Xml Size?
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Appreciated 5.8 years ago, created a post with more than 5 votes. For Parsing Ncbi Taxonomic Tree?
Good Question 5.8 years ago, asked a question that was upvoted at least 5 times. For Parsing Ncbi Taxonomic Tree?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Newbler And Ubuntu?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Parsing Ncbi Taxonomic Tree?
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Metagenomics Analysis
Student 5.8 years ago, asked a question with at least 3 up-votes. For Parsing Ncbi Taxonomic Tree?

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