User: jsporter

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jsporter60
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Posts by jsporter

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Get feature from location from gff3
... Something like this can be done with [gffutils][1]. This problem is similar to the [biostars post.][2] [1]: https://daler.github.io/gffutils [2]: https://www.biostars.org/p/357773/ ...
written 6 days ago by jsporter60
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Answer: A: Getting GFF annotation from sequence coordinates.
... Thanks for the help. The documentation for BCBio recommended [gffutils][1], and I was able to do what I wanted with gffutils. It creates a database of the gff file for efficiency, and it can handle some different specifications of gff files. import gffutils gff_in = "filename.gff" gff ...
written 6 days ago by jsporter60
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Comment: C: Getting GFF annotation from sequence coordinates.
... A package could generically be called a tool. Although a stand-alone program that does what I want would be useful as well. ...
written 6 days ago by jsporter60
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Comment: C: Getting GFF annotation from sequence coordinates.
... I am writing code to analyze the data in Python, so a tool in Python is desirable. This is not mutually exclusive with writing my own GFF parser/extractor tool since such a thing could exist. Why would I want to make my own if such a thing exists already? I have specific DNA sequences with coordi ...
written 6 days ago by jsporter60
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Answer: A: different bam from same NGS data
... The BAM file will not necessarily include the whole read from the original FASTQ file since it can be clipped, and this could lead to different alignment results. ...
written 6 days ago by jsporter60
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Getting GFF annotation from sequence coordinates.
... I am looking for a way to automate with Python looking up sequence annotations from a GFF file (or a GBFF file) from genomes stored by NCBI. I have a fasta file with kmers pulled from an NCBI genome. These kmers have coordinates such as the accession id, the contig id, and the start and end of the ...
ncbi python gff gene annotation written 6 days ago by jsporter60
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Answer: A: Gene Ontology -- Getting Complete Gene And Gene Ontology Term Associations
... Thanks for the response. The metabolicmine.org website did what I wanted. I found the program process-go from the Biorithim software package from T.M. Murali's lab that does the job as well. (http://bioinformatics.cs.vt.edu/~murali/software/biorithm/process-go.html) ...
written 5.5 years ago by jsporter60
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Answer: A: Correct Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
... mpiBlast can be used on a distributed memory architecture. ...
written 5.5 years ago by jsporter60
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Gene Ontology -- Getting Complete Gene And Gene Ontology Term Associations
... Hello, I want a way to generate a gene ontology term (GO term) and gene id association file. On the gene ontology website, I think I can get gene id and GO term associations, but only the most specific GO term is associated with the gene id. The web app Funcassociate2 (http://llama.mshri.on.ca/fu ...
python gene-ontology written 5.5 years ago by jsporter60
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Answer: A: How To Automatically Screen Thousands Of Sequences Using Vecscreen
... Okay, I got vecscreen to work. The problem was that the app wasn't included in the FTP files that I downloaded from NCBI. I used subversion to get all the code and was able to find and build vecscreen. The text output can be used to clean the sequences. This could be done with Python and BioPyth ...
written 5.7 years ago by jsporter60

Latest awards to jsporter

Scholar 6 days ago, created an answer that has been accepted. For A: How To Automatically Screen Thousands Of Sequences Using Vecscreen
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: How To Automatically Screen Thousands Of Sequences Using Vecscreen
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Difficulty Getting Ncbi Vecscreen
Popular Question 5.4 years ago, created a question with more than 1,000 views. For How To Automatically Screen Thousands Of Sequences Using Vecscreen
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Gene Ontology -- Getting Complete Gene And Gene Ontology Term Associations

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