Question: Repeted tandem in whole genome using Galaxy
1
gravatar for alejollanosl
22 months ago by
alejollanosl10
Universidad del Atlántico
alejollanosl10 wrote:

Hi everyone, it's my first post here.

I have no extensive knowledge on bioinformatics but, i wanna know how to compare repeated tandems in Leptospira's especies genomes.For that i already have download the genome whole genome from the NCBI portal, and make a UNION of the multiline fasta format to a single line fasta using a EMBOSS tool. but beyond that i really don't know how to procede. I know EMBOSS have tools to know repeated tandems, but i don't know how to compare the diferentes species.

So if you have a workflow or some suggestion, it would be a lo of help to me.

Thank you

Att Alejandro

alignment galaxy • 521 views
ADD COMMENTlink written 22 months ago by alejollanosl10

Hello,

This is not a Galaxy solution I am aware of (but this a literally a moving target and no one knows every detail of every tool/analysis path, and I am certainly not an exception). Perhaps you have reviewed the publications/online tool options already, but may be in in this sort detail, or were just asking of workflow exists already, and your question is about existing is to not waste time on duplicated effort. That said, not many online tools and reference data are proprietary or have licencing agreements, which will complicate including individual tools/workflow solutions within Galaxy. https://scholar.google.com/scholar?q=tandem+repeat+comparisons+across+genomes&hl=en&as_sdt=0&as_vis=1&oi=scholart&sa=X&ved=0ahUKEwjs3YK1tNfLAhVX3mMKHTT3Cb0QgQMIHjAA

I am not the best source for this analysis (new tools/methods are plentiful, always!) .. yet am also reviewing Galaxy tools/existing tutorials for this community'd analysis solutions to review options that are in Galaxy and NOT yet. There are almost always satisfactory analysis options - meaning, more that way to achieve a satisfactory result. In short, comparing methods/tool vs what is available in the Galaxy tool shed and public Galaxy instances in where to start. Any tool can be wrapped, and if not fully open source, licencing can often be worked out (agreement with tool/pipeline authors). https://usegalaxy.org/toolshed https://wiki.galaxyproject.org/PublicGalaxyServers

I am also asking for feedback from other Galaxy scientists directly. Will post more if a known workflow exists I missed. Meanwhile, please also explore as I describe above. It cannot harm, can be useful learn about different approaches even if you decide on a different path, plus ideas/requests/creation wrapped tools for unwrapped open-source or gaining granted access for academic use through agreements (tool form licence acknowledgement for academic-only use) are possible. The development of workflow for this analysis withing Galaxy (even if for use in a local/cloud Galaxy, not necessary http://usegalaxy.org) definitely seems worth it to me and perhaps other also interested in the same research.

Others that know more in this analysis area, please add in your knowledge even if partial (target tools/methods using Galaxy tools or other)! I have not done a review at other bioinformatics online resources (Biostars, Seqanswers, or even all Public Galaxies) - yet! This type of learning always interests me in general, as I suspect it would others in the Galaxy community.

Also keep in mind that Galaxy-using researchers are always coming up with parallel workflow solutions. If you yourself develop one, this could make for an interesting pub or publically shared resource to aid others.

The primary purpose of this comment is to open this up for discussion (knowledge sharing, in the spirit of scientists helping other scientist!) and to maybe entice others to participate.

Best with this! I'll share what I discover myself if find anything useful comes out, even if not a complete solution. Please also share back here after your review.

Jen, Galaxy team

ADD REPLYlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson23k

Hi Jen I just wanna tell you thanks for your encourage message. I am and i will work with this topic until i found some solution.

Thank you again.

Alejandro.

ADD REPLYlink written 22 months ago by alejollanosl10
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