User: Puli Chandramouli Reddy

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190
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Pune, India
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Posts by Puli Chandramouli Reddy

<prev • 41 results • page 2 of 5 • next >
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Comment: C: Identify Transcription factor from a list of genes
... Click on the number next to the GO term. ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Answer: A: Identify Transcription factor from a list of genes
... Hi, you can upload the list of the geneIDs in uniprot "retrieve/IDmapping" section and then you can browse by "gene ontology " under "View by" heading. Then you can go to "molecular_function" and "sequence-specific DNA binding" (transcription factor" and from here you can get list of transcription ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Comment: C: How to add GO pValue in blast2GO ?
... This is posted by mistake, ignore it. ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Comment: C: How to add GO pValue in blast2GO ?
... Easy way is to map your DEGs to zebrafish genes (find orthologues) and then you can use many of the tools which have zebrafish gene annotations (eg. [clusterProfiler][1]) [1]: https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Comment: C: Goat Genome gene prediction
... #after running maker merged gff file was used and first round of filtration was carried out by AED score cutoff. awk '{if($3=="mRNA")print$0}' ./base.all.gff |grep -v "trnascan"|grep "est2genome"| grep "mRNA-1"| grep "_AED=0.00"|grep "Name"|awk '{split($9,a,";");print a[2]}'|aw ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Comment: C: How to add GO pValue in blast2GO ?
... GO terms to all genes of you model organism. ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Comment: C: Goat Genome gene prediction
... what was the error when you run command for merging GFF. Also check in "base.maker.output/base_datastore", for gff files for individual contigs are present or not. ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Answer: A: How to add GO pValue in balst2GO ?
... Hi, You need to perform enrichment analysis of GO terms for DEGs over all GO terms to get p-values (can use BINGO). You can use just GO terms without p-values also but REVIGO will not give weightage based on p-values. ...
written 2.8 years ago by Puli Chandramouli Reddy190
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Comment: C: download nr database protein accession number to GO term file
... I have used InterProScan and it was fast enough to get the annotation. And also used BlastP (instead of Blast2Go) against UniRef90 (UniProt database) and output was used to make GAF file (GO annotation). I have combined the results from InterProScan and BlastP on UniRef90 and worked very well in i ...
written 2.9 years ago by Puli Chandramouli Reddy190
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Comment: C: download nr database protein accession number to GO term file
... Ok.. 1. One way is to map nr ids to uniprot and get associated GO ids (it may not work if your model organisms information is not there in UniProt). 2. Another way is to annotate you nr database by [InterProScan][1] or [Blast2Go][2]. [1]: https://www.ebi.ac.uk/interpro/interproscan.html [2 ...
written 2.9 years ago by Puli Chandramouli Reddy190

Latest awards to Puli Chandramouli Reddy

Scholar 19 months ago, created an answer that has been accepted. For A: Goat Genome gene prediction
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Fetching NCBI gene symbols from NCBI protein ids or GI identifiers
Scholar 2.9 years ago, created an answer that has been accepted. For A: Goat Genome gene prediction

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