User: Ric
Ric • 300
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- Australia
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- 7 hours ago
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Posts by Ric
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... 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 ...
written 7 hours ago by
Ric • 300
• updated
7 hours ago by
Pierre Lindenbaum ♦ 131k
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... 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 ...
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... How did you map your genes against Plant Reactome? ...
written 6 weeks ago by
Ric • 300
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... 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 ...
written 6 weeks ago by
Ric • 300
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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
Ric • 300
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... 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 ...
written 7 weeks ago by
Ric • 300
0
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... Hi,
InterProScan seems only to support Humans. Is there any similar tool for plants?
Thank you in advance, ...
written 8 weeks ago by
Ric • 300
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... 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,
...
written 9 weeks ago by
Ric • 300
2
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... 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,
...
written 10 weeks ago by
Ric • 300
• updated
10 weeks ago by
toralmanvar • 900
1
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1
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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
Ric • 300
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