about fix length

[pariswu1988]

hi, could please help how to make fix length sequence?

[cjjong23]

Yes, does anyone have any suggestions on making the same width sequences? And, where do you guys get the human reference database?

[arunhpatil]

For proteomics data, you could refer to PTM-Pro . In FAQs you can download protein databases of few model organsims and can also get fix length sequence upon using the tool. let me know if you need any further information.

[pariswu1988]

For proteomics data, you could refer to PTM-Pro . In FAQs you can download protein databases of few model organsims and can also get fix length sequence upon using the tool. let me know if you need any further information.

hi, yes, I can find the databases of arabidopsis but ca not find the tool to get fix length. That will be very kind of you if give this info. Thanks a lot!

[arunhpatil]

Sure. Can you send me a sample file with protin accession and the site of modification. I will setup a module to fetch the fixed lenth window of 15 aa.

[cjjong23]

Hi Arun,

Thanks for the info. I have a question though, I am searching for human

protein databases. Which one in the databases would you recommend? Thank you so much.

On Thu, Apr 25, 2019 at 7:56 AM Arun Patil [email protected] wrote:

For proteomics data, you could refer to PTM-Pro http://ptm-pro.inhouseprotocols.com/ . In FAQs you can download protein databases of few model organsims and can also get fix length sequence upon using the tool. let me know if you need any further information.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/omarwagih/rmotifx/issues/6#issuecomment-486660990, or mute the thread https://github.com/notifications/unsubscribe-auth/ALVKUEYL5MFIMF4XHOCOFP3PSGTBFANCNFSM4HGQMATA .

[arunhpatil]

Hi. According to literature, neXtProt https://www.nextprot.org/and RefSeq https://www.ncbi.nlm.nih.gov/refseq/ are widely used databases in the community. Both are updated frequently. At PTM-Pro, we have the recent version RefSeq 92, you may use that. You can download databases currently indexed on the server from here. http://ptm-pro.inhouseprotocols.com/Databases/

Arun.

On Wed, May 8, 2019 at 8:02 PM cjjong23 [email protected] wrote:

Hi Arun,

Thanks for the info. I have a question though, I am searching for human protein databases. Which one in the databases would you recommend? Thank you so much.

On Thu, Apr 25, 2019 at 7:56 AM Arun Patil [email protected] wrote:

For proteomics data, you could refer to PTM-Pro http://ptm-pro.inhouseprotocols.com/ . In FAQs you can download protein databases of few model organsims and can also get fix length sequence upon using the tool. let me know if you need any further information.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/omarwagih/rmotifx/issues/6#issuecomment-486660990, or mute the thread < https://github.com/notifications/unsubscribe-auth/ALVKUEYL5MFIMF4XHOCOFP3PSGTBFANCNFSM4HGQMATA

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[cjjong23]

Hi Arun,

I am sorry to keep bothering you. Since I am interested in using the

rmotifx, is there a way I can pre-align all the background sequences? Thank you so much again for your advice.

On Thu, May 9, 2019 at 1:52 AM Arun Patil [email protected] wrote:

Hi. According to literature, neXtProt https://www.nextprot.org/and RefSeq https://www.ncbi.nlm.nih.gov/refseq/ are widely used databases in the community. Both are updated frequently. At PTM-Pro, we have the recent version RefSeq 92, you may use that. You can download databases currently indexed on the server from here. http://ptm-pro.inhouseprotocols.com/Databases/

Arun.

On Wed, May 8, 2019 at 8:02 PM cjjong23 [email protected] wrote:

Hi Arun,

Thanks for the info. I have a question though, I am searching for human protein databases. Which one in the databases would you recommend? Thank you so much.

On Thu, Apr 25, 2019 at 7:56 AM Arun Patil [email protected] wrote:

For proteomics data, you could refer to PTM-Pro http://ptm-pro.inhouseprotocols.com/ . In FAQs you can download protein databases of few model organsims and can also get fix length sequence upon using the tool. let me know if you need any further information.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/omarwagih/rmotifx/issues/6#issuecomment-486660990 , or mute the thread <

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[arunhpatil]

Hi.

You could download the pre-aligned data from phosphosite plus https://www.phosphosite.org/homeAction.action for your organism of interest and extract the PTM-window.

I hope this helps.

Arun.

On Mon, May 13, 2019 at 11:13 PM cjjong23 [email protected] wrote:

Hi Arun,

I am sorry to keep bothering you. Since I am interested in using the rmotifx, is there a way I can pre-align all the background sequences? Thank you so much again for your advice.

On Thu, May 9, 2019 at 1:52 AM Arun Patil [email protected] wrote:

Hi. According to literature, neXtProt https://www.nextprot.org/and RefSeq https://www.ncbi.nlm.nih.gov/refseq/ are widely used databases in the community. Both are updated frequently. At PTM-Pro, we have the recent version RefSeq 92, you may use that. You can download databases currently indexed on the server from here. http://ptm-pro.inhouseprotocols.com/Databases/

Arun.

On Wed, May 8, 2019 at 8:02 PM cjjong23 [email protected] wrote:

Hi Arun,

Thanks for the info. I have a question though, I am searching for human protein databases. Which one in the databases would you recommend? Thank you so much.

On Thu, Apr 25, 2019 at 7:56 AM Arun Patil [email protected] wrote:

For proteomics data, you could refer to PTM-Pro http://ptm-pro.inhouseprotocols.com/ . In FAQs you can download protein databases of few model organsims and can also get fix length sequence upon using the tool. let me know if you need any further information.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/omarwagih/rmotifx/issues/6#issuecomment-486660990 , or mute the thread <

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[arunhpatil]

Hi,

We have updated the version of PTM-Pro http://ptm-pro.inhouseprotocols.com/, a software tool to analyze multiple post-translational modifications. The second version (PTM-Pro2.0) includes lot of additional features. Check out and share accross with the members of your Institute, group, and friends for an extended reach for the use of PTM-Pro and to further improve this user-friendly open-source tool.

URL: http://ptm-pro.inhouseprotocols.com/

If you have any queries or suggestions please write to [email protected].

In case, If you use the PTM-Pro tool, plesae cite the following: Patil, A. H., Datta, K. K., * et al*., Dissecting Candida pathobiology: Post-translational modifications on the Candida tropicalis proteome. 2018. * OMICS: A Journal of Integrative Biology*. [PubMed]. https://www.ncbi.nlm.nih.gov/pubmed/30106353

Thank you, Arun.

On Mon, May 13, 2019 at 11:13 PM cjjong23 [email protected] wrote:

Hi Arun,

I am sorry to keep bothering you. Since I am interested in using the rmotifx, is there a way I can pre-align all the background sequences? Thank you so much again for your advice.

On Thu, May 9, 2019 at 1:52 AM Arun Patil [email protected] wrote:

Hi. According to literature, neXtProt https://www.nextprot.org/and RefSeq https://www.ncbi.nlm.nih.gov/refseq/ are widely used databases in the community. Both are updated frequently. At PTM-Pro, we have the recent version RefSeq 92, you may use that. You can download databases currently indexed on the server from here. http://ptm-pro.inhouseprotocols.com/Databases/

Arun.

On Wed, May 8, 2019 at 8:02 PM cjjong23 [email protected] wrote:

Hi Arun,

Thanks for the info. I have a question though, I am searching for human protein databases. Which one in the databases would you recommend? Thank you so much.

On Thu, Apr 25, 2019 at 7:56 AM Arun Patil [email protected] wrote:

For proteomics data, you could refer to PTM-Pro http://ptm-pro.inhouseprotocols.com/ . In FAQs you can download protein databases of few model organsims and can also get fix length sequence upon using the tool. let me know if you need any further information.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/omarwagih/rmotifx/issues/6#issuecomment-486660990 , or mute the thread <

https://github.com/notifications/unsubscribe-auth/ALVKUEYL5MFIMF4XHOCOFP3PSGTBFANCNFSM4HGQMATA

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[omarwagih]

@pariswu1988 you can use the msa package: https://bioconductor.org/packages/release/bioc/html/msa.html to pre-align your sequences.