User: anu014

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anu014140
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India
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2 years, 6 months ago
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Posts by anu014

<prev • 114 results • page 1 of 12 • next >
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Comment: C: How to get Gene symbols & nuclotide FASTA for taxid :1239
... Still it's not working @GenoMax. After running this it's showing me 'help' of efetch : EFETCH - retrieve entries from sequence databases. Synopsis: efetch -options [database:] Databases: SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite Options: -a Search wi ...
written 2 days ago by anu014140
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Comment: C: How to get Gene symbols & nuclotide FASTA for taxid :1239
... Okay I got it now. One can download edirect suit from here : ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/ . It contains esearch n efetch programs. ...
written 2 days ago by anu014140
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Comment: C: How to get Gene symbols & nuclotide FASTA for taxid :1239
... I know it's primitive question but how to download esearch? It's throwing error : 'No command 'esearch' found' ... ...
written 2 days ago by anu014140
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Comment: C: How to get Gene symbols & nuclotide FASTA for taxid :1239
... I want gene symbols n fasta sequences if input is refseq protein ids for taxon id 1239. ...
written 3 days ago by anu014140
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How to get Gene symbols & nuclotide FASTA for taxid :1239
... Hello Biostars! I was trying to get Gene symbols for taxon 1239 (Firmicutes) from refseq_protein ids, but was unable to do so using Biodbnet (https://biodbnet-abcc.ncifcrf.gov/db/db2db.php). Eg. 'WP_020487904.1' (https://www.ncbi.nlm.nih.gov/protein/521976633/). Even gene2refseq file - ftp://ftp.n ...
gene genome sequence written 3 days ago by anu014140 • updated 7 hours ago by tdmurphy70
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Download CAZy database
... Hello Biostars, Can anyone tell me how to download CAZy database ? http://www.cazy.org/ Or is it even accessible ? Please help. Thanks in advance. :) ...
genome gene database cazy written 8 days ago by anu014140 • updated 8 days ago by h.mon11k
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Comment: C: GO Annotations from geneontology.org
... Right now, I'm dealing with 'mycobacterium tuberculosis h37rv' & 'mus musculus'. For mouse, I see GO & KEGG codes but for mycobacterium tuberculosis h37rv I'm just getting KEGG code.. How is this even possible, KEGG but no GO ? ...
written 18 days ago by anu014140
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Comment: C: GO Annotations from geneontology.org
... Hello EagleEye. Thanks for suggestion! But for custom database/ non-model organisms I've to create GO/KEGG files as explained by you here - https://www.biostars.org/p/150137/#150175 . Again, I've to go to the source such as 'geneontology.org' to get GO entries & their associated Genes.. Is ther ...
written 19 days ago by anu014140
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GO Annotations from geneontology.org
... Hello Biostars! Can anyone tell me how to get GO Ontology (Molecular function, Cellular Component & Biological process ) along with genes involved in it from GAF (go-annotation-file) or geneontology.org for a particular species? Right now I'm getting from GAF: Column Content Required? ...
gene genome next-gen written 22 days ago by anu014140 • updated 22 days ago by EagleEye4.9k
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Getting MDSplot from Cufflinks data [cummeRbund]
... Hello Biostars, I am doing MDSplot like this : library(cummeRbund) cuff<-readCufflinks(gtfFile="merged.gtf",genome="grch38") cuff CuffSet instance with: 2 samples 56875 genes 282953 isoforms 131485 TSS 81720 CDS 56875 promoters 131485 s ...
R next-gen rna-seq written 23 days ago by anu014140 • updated 14 days ago by Kevin Blighe13k

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Centurion 25 days ago, created 100 posts.
Voter 3 months ago, voted more than 100 times.
Supporter 11 months ago, voted at least 25 times.

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