User: Shred

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Shred60
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Posts by Shred

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Find all sequence of a specific genus amplified by a couple of primers
... Thanks. What if I've already got an amplicon and I want to do a DB of all the amplicons obtained from? I've thought this way: 1) Build a reference database of the region of every known genome of the family 2) Blast the amplicon against this DB 3) Use the sstart and ssend to trim the seq ...
written 8 weeks ago by Shred60
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Find all sequence of a specific genus amplified by a couple of primers
... Is there a way to find every sequence present in a database amplified by a couple of custom primers? I've designed two primers to amplify a variable region of the genome of a Staphylococcus, and I want to look how many references sequence were amplified by this couple of primers. Is there an online ...
alignment sequence primer pcr written 8 weeks ago by Shred60
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Answer: A: Get taxonomy into a CDS from genomic custom database
... Here's my solution. Actually, it's better using that on Blast results, rather than on the assembled fasta, because it's written in bash, so it will become extremely slow with huge file. while read line ; do PROTEINID=$( echo $line | sed -e 's/.*protein_id\=\(.*\)\]\ \[location.*/\1/' ) ...
written 10 weeks ago by Shred60
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Comment: C: Get taxonomy into a CDS from genomic custom database
... Thanks a lot. Using the service you've linked, I've found a quick way to solve my task. $ wget -qO- http://togows.org/entry/ncbi-protein/PVV28006.1/definition | sed 's/^.*[//;s/]$// Using a while read loop, I've used the protein id as a variable, and imported it every time into a different w ...
written 10 weeks ago by Shred60
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Comment: C: Get taxonomy into a CDS from genomic custom database
... Thanks, but it's not a single species but a single genus. It is possible to download a taxid file specific to the genus "Bifidobacterium" , instead of downloading the whole taxid file from ncbi? ...
written 10 weeks ago by Shred60
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Comment: C: Get taxonomy into a CDS from genomic custom database
... Yes, what I want actually is scientific name of each record. I want to do that in order to get scientific name using "stitle" parameter option in blastn output, in a database created from this edited fasta file. ...
written 10 weeks ago by Shred60
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Comment: C: Get taxonomy into a CDS from genomic custom database
... Question updated. I've appended taxonomy at end of the header, but actually is not a priority itself. ...
written 10 weeks ago by Shred60
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Get taxonomy into a CDS from genomic custom database
... Guys, I know this question got similarities with older posts here, but I'm stuck on getting a solution. I've got this situation: I've downloaded from ncbi assembly a bacterial genus specific database made with the nucleotide sequences of genes, using the "CDS from genomic" option. While getting the ...
#ncbi #taxonomy #database #genomic written 10 weeks ago by Shred60
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Answer: A: Perl script required
... Don't need to be in perl. If you're working with tab separated values (so outfmt 6) , you can easly do a filter with awk. Assuming evalue is on the 4th column, thìs command will print only lines where evalue is *lower* than 0.02 awk -F'\t' '$4 < 0.02 {print ;}' Same things could be done wi ...
written 3 months ago by Shred60
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Comment: C: Display full information about taxa instead of staxids in BLASTn
... I'm looking for scientific names. I've tried using ssciname, but I still don't get the wanted results. ...
written 4 months ago by Shred60

Latest awards to Shred

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How can I find the same record in two file? Use python
Scholar 5 months ago, created an answer that has been accepted. For A: Faster way to get GC content and Coverage from .fasta

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