User: saadleeshehreen

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Posts by saadleeshehreen

<prev • 79 results • page 1 of 8 • next >
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How to fetch sequences from Proteinortho5 output containing all test species and no duplication in each genome
... Hi, I want to construct a phylogenic tree on 100 *Pseudomonas aeruginosa* genomes. Before constructing the tree, I want to first cluster those genomes on the basis of homology and for this purpose, I am using ProteinOrtho5 software. After running the software with synteny option I want to extract pr ...
proteinortho5 written 8 weeks ago by saadleeshehreen60 • updated 8 weeks ago by h.mon23k
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Counting base and nucleotide frequency of multifasta file
... Hi, I have a mulifasta with 2000 sequences. The file is like this. >spacer_1 ATCCCGGGGGGTTTA............... >spacer_2 TCAGGTTT....... . . I want to count how many bases for each of them and what is the frequency of nucleotide (A,T,G,C) in each of the sequence. I tried ...
multifasta base count nucleotide frequency written 10 weeks ago by saadleeshehreen60 • updated 10 weeks ago by Firas0
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Comment: C: Problem to run a perl script from shell
... same error message is showing ...
written 10 weeks ago by saadleeshehreen60
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(Closed) Problem to run a perl script from shell
... Hi, why the error is given though the file is here -bash-4.2$ ls fna_PA.ls resfinder.pl tmp -bash-4.2$ perl resfinder.pl Error: No such file or directory How to solve the problem? ...
perl written 10 weeks ago by saadleeshehreen60
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Comment: C: How to install CRISPRdisco
... Thanks for suggestions. I have contacted them and waiting for the response. ...
written 10 weeks ago by saadleeshehreen60
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How to install CRISPRdisco
... I am trying to install the software on our server (https://github.com/CRISPRlab/CRISPRdisco ). I have no root permission to install any software and I am unfamiliar with docker. So, I tried to follow the instruction written under **To install by hand** to install the software. While trying to run wi ...
docker written 10 weeks ago by saadleeshehreen60 • updated 10 weeks ago by Michael Dondrup45k
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Install CRISPRCasFinder under Ubuntu without having administrator rights
... Hi, I need to install the following software in our server. https://crisprcas.i2bc.paris-saclay.fr/Home/Download Our server uses linux operating system but I don't have administrator rights. I usually use conda to install any software but this particular one doesn't have conda version. How can I in ...
crispr install linux written 10 weeks ago by saadleeshehreen60 • updated 10 weeks ago by WouterDeCoster36k
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Comment: C: How to retrieve information on bacterial source from NCBI?
... One solution, I have just got: esearch -db assembly -query GCF_000647595.2 | elink -related -cmd neighbor -name assembly_biosample | xml2 | grep "/eLinkResult/LinkSet/LinkSetDb/Link/Id=" | awk 'BEGIN{FS="="} {print $2}' You just need a xml2 to download. ...
written 11 weeks ago by saadleeshehreen60
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Comment: C: How to retrieve information on bacterial source from NCBI?
... Thanks for that. It works for me, but I got only 1000 results. I have a table with all assembly_ID (eg. GCF_000006765) of *Pseudomonas aeruginosa*, so I need to map back this table. How can I map back assembly id with biosample accession? ...
written 11 weeks ago by saadleeshehreen60
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How to retrieve information on bacterial source from NCBI?
... Hi, I want to get the isolation source (clinical/environmental) information for all RefSeq *Pseudomonas aeruginosa* genomes. Roughly, I know around 2000 sequenced *Pseudomonas aeruginosa* are available in NCBI. Sometimes the isolation source are mentioned in the Biosample e.g. https://www.ncbi.nlm ...
ncbi bacteria isolationsource retrieve written 11 weeks ago by saadleeshehreen60 • updated 11 weeks ago by vkkodali910

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