User: Ric

gravatar for Ric
Ric300
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Australia
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7 hours ago
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8 years, 9 months ago
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Posts by Ric

<prev • 271 results • page 1 of 28 • next >
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Removing a DOT after each sequence
... Hi, I have a FASTA file which contains a `.` after each sequence. How is it possilble to remove the dot? >gene39576 gene=rps16 MVKLRLKRCGRKQRAVYRIVAIDVRSRREGKDLRKVGFYDPIKNQTYLNVPAILYFLEKG AQPTGTVQDILKKAEVFKELRPNQS. >gene39578 gene=psbK MLNTFSLIGICLNSTLFSSSFFFGKLPEAYAFLNPIV ...
sequence bioawk written 7 hours ago by Ric300 • updated 7 hours ago by Pierre Lindenbaum131k
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GO annotations into GFF3
... Hi, I would like to add `GO term` into the GFF3 and I found the following mapping file (`goa_uniprot_all.gpa`). gpa-version: 1.1 ! !This file contains all GO annotations for proteins in the UniProt KnowledgeBase (UniProtKB). ! !It also contains all annotations for protein comple ...
annotation go written 12 days ago by Ric300 • updated 12 days ago by JC12k
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Comment: C: Reactome Plant to Cytoscape - possible?
... How did you map your genes against Plant Reactome? ...
written 6 weeks ago by Ric300
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Reactome for Plants
... Hi, I downloaded the mapping files from [Plant Reactome][1]. How is it possible to map Reactome ids ==> NCBI2PlantReactome_PE_Pathway.txt <== A0A1R3FTW0 R-COL-9609608-16 A0A1R3FTW0 [cytosol] R-COL-9609573 https://plantreactome.gramene.org/PathwayBrowser/#/R-COL-9609573 Tricin biosynth ...
pathway gene annotation written 6 weeks ago by Ric300
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Comment: C: InterProScan for Plants
... For example, if Pathway analysis is enabled in InterProScan then it provides for Reactome a Human id `R-HSA-5689880` which can be viewed [here][1]. However, I would prefer that the software uses [Plant Reactome][2]. Is there a way to change InterProScan behaviour? [1]: https://reactome.org/Pathwa ...
written 7 weeks ago by Ric300
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Non redundant ID associating with GO and Pathway
... Hi, I ran Blast/diamond with our plant protein sequence against [NR][1]. In the result file I saw different types of IDs: XP_015159008.1 PHT27876.1 XP_009768969.1 XP_016509492.1 XP_016509492.1 OIT28878.1 XP_019240799.1 XP_009595915.1 OIT08863.1 XP_016514212 ...
pathway alignment go written 7 weeks ago by Ric300
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InterProScan for Plants
... Hi, InterProScan seems only to support Humans. Is there any similar tool for plants? Thank you in advance, ...
gene annotation protein pathways ontology written 8 weeks ago by Ric300
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Finding common and different genes between species
... Hi, We have two plants which one of them is the wild type. For each of them, I used the Scallop results with TransDecoder. How is possible to determine which are common and different genes between those two plants from Scallop/Transdecoder results? Thank you in advance, ...
gene annotation rna-seq written 9 weeks ago by Ric300
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pathway analysis in plants
... Hi, We have de-novo assembled a non-model plant genome, and we also annotated it by ourselves. Which tools are recommended to do pathway analysis? Thank you in advance, ...
gene assembly analysis annotation pathway written 10 weeks ago by Ric300 • updated 10 weeks ago by toralmanvar900
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Answer: A: annotation with Augustus
... Has been answered [here](https://github.com/Gaius-Augustus/Augustus/issues/178) ...
written 11 weeks ago by Ric300

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Popular Question 2 days ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Popular Question 16 days ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Scholar 11 weeks ago, created an answer that has been accepted. For A: topGo Error in .local(.Object, ...) : allGenes must be a factor with 2 levels
Popular Question 12 weeks ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
Epic Question 12 weeks ago, created a question with more than 10,000 views. For How to calculate the insert size for Paired-end reads
Great Question 3 months ago, created a question with more than 5,000 views. For How to calculate the insert size for Paired-end reads
Popular Question 3 months ago, created a question with more than 1,000 views. For How to install NGS: Indel Analysis>Indel Analysis in Galaxy
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