[biomart-users] Batch download of FASTA seq with an input file of JGI IDs on Phytozome

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SI
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[biomart-users] Batch download of FASTA seq with an input file of JGI IDs on Phytozome

SI
Hi,

I have 996 JGI sequence IDs in a text file, for which I would like to carry out a batch download of FASTA sequences.
Would be of great help if someone could let me know how I could do that on Phytozome-Biomart.
Thanks in advance for your time,
Best
SI

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Re: [biomart-users] Batch download of FASTA seq with an input file of JGI IDs on Phytozome

David M. Goodstein
SI, could you show me an example of the identifiers you are working with?  It is usually straightforward to upload a set of text ids into Phytozome's BioMart but there are sometimes issues with id's from older genome versions, and some ambiguity as to what is a transcript vs locus identifier.

best,
-David


On Wed, Nov 22, 2017 at 6:31 AM, SI <[hidden email]> wrote:
Hi,

I have 996 JGI sequence IDs in a text file, for which I would like to carry out a batch download of FASTA sequences.
Would be of great help if someone could let me know how I could do that on Phytozome-Biomart.
Thanks in advance for your time,
Best
SI

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David M. Goodstein, Ph.D.
Phytozome and Plant Comparative Analysis Group Lead
Joint Genome Institute - U.S. Dept. of Energy

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SI
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Re: [biomart-users] Batch download of FASTA seq with an input file of JGI IDs on Phytozome

SI
Hi David,

A subset of identifiers are as follows:
58178
58140
184242
574
137300
56237
55336
55286
55270
55268
55098
54374
5437
53583
53522

Do these look ok to you?

Thanks
Indu

On Wednesday, November 22, 2017 at 10:29:36 PM UTC, dmgoodstein wrote:
SI, could you show me an example of the identifiers you are working with?  It is usually straightforward to upload a set of text ids into Phytozome's BioMart but there are sometimes issues with id's from older genome versions, and some ambiguity as to what is a transcript vs locus identifier.

best,
-David


On Wed, Nov 22, 2017 at 6:31 AM, SI <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="G08XEbCPAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">indug...@...> wrote:
Hi,

I have 996 JGI sequence IDs in a text file, for which I would like to carry out a batch download of FASTA sequences.
Would be of great help if someone could let me know how I could do that on Phytozome-Biomart.
Thanks in advance for your time,
Best
SI

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David M. Goodstein, Ph.D.
Phytozome and Plant Comparative Analysis Group Lead
Joint Genome Institute - U.S. Dept. of Energy
<a href="http://phytozome.jgi.doe.gov" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fphytozome.jgi.doe.gov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_e6p6BuiXRS-d7db8beHYzU3cgg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fphytozome.jgi.doe.gov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_e6p6BuiXRS-d7db8beHYzU3cgg&#39;;return true;">http://phytozome.jgi.doe.gov

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Re: [biomart-users] Batch download of FASTA seq with an input file of JGI IDs on Phytozome

David M. Goodstein
Those purely numerical identifiers look like they’re from a very old version of a plant annotation that got migrated to Phytozome later. What is the organism?

David M. Goodstein
Joint Genome Institute
Lawrence Berkeley National Lab
U.S. Dept. of Energy

On Nov 23, 2017, at 1:41 AM, SI <[hidden email]> wrote:

Hi David,

A subset of identifiers are as follows:
58178
58140
184242
574
137300
56237
55336
55286
55270
55268
55098
54374
5437
53583
53522

Do these look ok to you?

Thanks
Indu

On Wednesday, November 22, 2017 at 10:29:36 PM UTC, dmgoodstein wrote:
SI, could you show me an example of the identifiers you are working with?  It is usually straightforward to upload a set of text ids into Phytozome's BioMart but there are sometimes issues with id's from older genome versions, and some ambiguity as to what is a transcript vs locus identifier.

best,
-David


On Wed, Nov 22, 2017 at 6:31 AM, SI <[hidden email]> wrote:
Hi,

I have 996 JGI sequence IDs in a text file, for which I would like to carry out a batch download of FASTA sequences.
Would be of great help if someone could let me know how I could do that on Phytozome-Biomart.
Thanks in advance for your time,
Best
SI

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David M. Goodstein, Ph.D.
Phytozome and Plant Comparative Analysis Group Lead
Joint Genome Institute - U.S. Dept. of Energy

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SI
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Re: [biomart-users] Batch download of FASTA seq with an input file of JGI IDs on Phytozome

SI
They are from Chlamydomonas reinhardtii. They were retrieved from the following reference:

The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features
Mia Terashima • Michael Specht • Michael Hippler
Curr Genet (2011) 57:151–168

So, they could not be from a version newer than 2011.

Indu

On Thursday, November 23, 2017 at 5:30:40 PM UTC, dmgoodstein wrote:
Those purely numerical identifiers look like they’re from a very old version of a plant annotation that got migrated to Phytozome later. What is the organism?

David M. Goodstein
Joint Genome Institute
Lawrence Berkeley National Lab
U.S. Dept. of Energy

On Nov 23, 2017, at 1:41 AM, SI <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="loi7v_TNAgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">indug...@...> wrote:

Hi David,

A subset of identifiers are as follows:
58178
58140
184242
574
137300
56237
55336
55286
55270
55268
55098
54374
5437
53583
53522

Do these look ok to you?

Thanks
Indu

On Wednesday, November 22, 2017 at 10:29:36 PM UTC, dmgoodstein wrote:
SI, could you show me an example of the identifiers you are working with?  It is usually straightforward to upload a set of text ids into Phytozome's BioMart but there are sometimes issues with id's from older genome versions, and some ambiguity as to what is a transcript vs locus identifier.

best,
-David


On Wed, Nov 22, 2017 at 6:31 AM, SI <[hidden email]> wrote:
Hi,

I have 996 JGI sequence IDs in a text file, for which I would like to carry out a batch download of FASTA sequences.
Would be of great help if someone could let me know how I could do that on Phytozome-Biomart.
Thanks in advance for your time,
Best
SI

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--
David M. Goodstein, Ph.D.
Phytozome and Plant Comparative Analysis Group Lead
Joint Genome Institute - U.S. Dept. of Energy
<a href="http://phytozome.jgi.doe.gov" rel="nofollow" target="_blank" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fphytozome.jgi.doe.gov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_e6p6BuiXRS-d7db8beHYzU3cgg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fphytozome.jgi.doe.gov\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF_e6p6BuiXRS-d7db8beHYzU3cgg&#39;;return true;">http://phytozome.jgi.doe.gov

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