User: steven

gravatar for steven
steven70
Reputation:
70
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Trusted
Location:
United States
Last seen:
3 years, 10 months ago
Joined:
4 years, 5 months ago
Email:
s*********@gmail.com

University of Connecticut cs major

Posts by steven

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Extract subset sequences from fasta file
... 1. iterate through the lines in the file 2. if the line starts with `>` check if length > 300 - if it is, check if loc=2R or loc=2L and print until the next sequence header `>` - if not, do nothing ...
written 4.3 years ago by steven70 • updated 9 days ago by RamRS24k
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Comment: C: Annotating gene symbols with BioPython
... post your code.. ...
written 4.3 years ago by steven70
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Comment: C: Blast 2.2.31+ "makeblastdb": where are my databases?
... try running makeblastdb again but this time specify a full path for the output directory ...
written 4.4 years ago by steven70
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Comment: C: Blast 2.2.31+ "makeblastdb": where are my databases?
... did you perform a search for the file name on the entire system? check the `C:\` and the `C:\Program Files\NCBI\blast-2.2.31+` directories specifically ...
written 4.4 years ago by steven70 • updated 8 days ago by RamRS24k
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Comment: C: Matching and extracting fasta sequences using shell script
... I'm not sure if this website is like Stackoverflow, but you should really post what you tried instead of just asking people to do your work for you. It looks like you did not try anything at all, and while many people on this site don't have much programming experience, this is a relatively simple t ...
written 4.4 years ago by steven70
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Comment: C: Tools to find the unique proteins (without orthologs) in a bacterial taxon
... Hi Natasha, the nice thing about usearch is that it compares each sequence to the other sequences in the file - so you don't need a reference file with unique proteins. So maybe try: usearch --cluster_fast input.fasta --id 1.0 --centroids output.fasta where input.fasta is the database of proteins ...
written 4.4 years ago by steven70
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Comment: C: Tools to find the unique proteins (without orthologs) in a bacterial taxon
... Hi Natasha, sorry I wasn't very specific in my previous comment. 0.70 is the recommended id for proteins when clustering. Here is the man page for id: http://drive5.com/usearch/manual/opt_id.html I think if the id is set to 1.0 (sequences must be 100% matching), the sequences can be clustered into ...
written 4.4 years ago by steven70
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Comment: C: Tools to find the unique proteins (without orthologs) in a bacterial taxon
... I'd recommend using Usearch: usearch --cluster_fast proteins.fasta --id 0.70 --centroids proteins_centroids.fasta ...
written 4.4 years ago by steven70
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Hybrid assembly with MiSeq and PacBio reads in ABySS
... I have a set of paired end and single end MiSeq Illumina reads: Sample_1.fastq, Sample_2.fastq, Sample_s.fastq If I wanted to assemble this with Abyss it would be: abyss-pe K=Kmer name=Sample_Kmer in='Sample_1.fastq Sample_2.fastq' se='Sample_s.fastq' Now I want to perform a hybrid assembly with ...
assembly written 4.4 years ago by steven70 • updated 4.4 years ago by h.mon28k
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Comment: C: Maker annotation failure
... thanks, well i got the "Maker has completed !" message so looks like everything worked out ...
written 4.4 years ago by steven70

Latest awards to steven

Scholar 4.4 years ago, created an answer that has been accepted. For A: How do I load more than 200 nucleotide EST sequences into fasta files from NCBI
Supporter 4.4 years ago, voted at least 25 times.
Scholar 4.4 years ago, created an answer that has been accepted. For A: How do I load more than 200 nucleotide EST sequences into fasta files from NCBI

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