Trematode.net User Support

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John Martin

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Jul 9, 2014, 7:26:14 PM7/9/14
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This topic is for asking questions and seeking help with the use of the Trematode.net website.

poma...@gmail.com

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Aug 5, 2015, 6:10:24 AM8/5/15
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Hi Trematode.net team!!

Is it possible to download the KEGG annotation data used in TremaPath? To imploy comparisons I need this in machine-readable format without using the browser interface.

Best wishes,
Mike

John Martin

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Aug 5, 2015, 9:00:40 PM8/5/15
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Hi Mike,
    I believe the TremaGene KEGG annotations were made using KEGG release 68.0, which is only available via a subscription to KEGG.  The best I could provide you would be a copy of the last publicly available KEGG genes db release, which was v58 (I think from 2012).  If that would be helpful to you let me know.   But if you absolutely need v68 that was used to annotated TremaGene, you'll need to look into your own subscription to KEGG:

http://www.bioinformatics.jp/en/keggftp.html

Note that v68 itself is fairly old now, I think the current release is up to v75.0 (July 2015).


poma...@gmail.com

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Aug 6, 2015, 12:27:12 AM8/6/15
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What I currently need is a pretty specific thing for which I believe no subscriptions are needed. In the paper about Nemapath you write:
--
"Plaintext file versions of alignment information (as compiled by KEGGscan) are also available by species http://www.nematode.net/FTP/nemapath_ftp/index.php"...
--

I can run a program like KOBAS on Clonorchis sinensis, and Opisthorchis viverrini (species I need data for) but a better way would be to use external source with manual curation and just cite it. The link you provide in the paper seem to contain KEGG annotation for specific species and that is what I need but it is broken.

John Martin

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Aug 6, 2015, 3:51:42 PM8/6/15
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Ah, sorry for my misunderstanding.  I can share the annotations we made to those genesets.  I've attached the KEGG v68 annotations made to the C.sinensis geneset to this post.   I will need to check with a colleague to locate the O.viverrini annotations, but I will post them once I find them as well.

The tab-delimited column format is:

1- species
2- gene identifier
3- species from which the gene being hit originated
4- e-value
5- bitscore
6- description of gene being hit
7- type of entity being hit (should always be gene in this file)
8- K0 id assigned based on this homology


Thanks,
John



Clonorchis_sinensis-KEGGv68.tsv.gz

poma...@gmail.com

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Aug 7, 2015, 12:17:13 AM8/7/15
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Hi John,

That is just what I need. Let me know if O. viverrini data is available.

Thanks,
Mike

John Martin

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Aug 10, 2015, 4:19:09 PM8/10/15
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Sorry for the delay.  Here are the KEGG annotations for O.viverrini.   Let me know if you have questions.


Thanks,
John

Opisthorchis_viverrini-KEGGv68.tsv.gz

potsg...@gmail.com

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Sep 27, 2019, 5:48:12 PM9/27/19
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72406418_938247763210011_8152915686742556672_n.jpg

how can I post a photo..of something that I need to be identified.??? I tried to drag and drop but it wouldn't let me do it
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