Logo tool in Galaxy

Hi!

I have a sequnce logo of an miRNA, that gives me no output? All the steps are done correctly in Galaxy sequnce logo tool. What can be evaluated on such an output?

No conservation?

Thanks!

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Welcome, @A_T!

Is this the tool being used? Sequence Logo generator for fasta (eg Clustal alignments) (Galaxy Version 3.5.0)

The input requirements are very specific. Review the tool help and compare your data. Does your multiple alignment fasta meet the expected formatting?

If so, and you are working at a public Galaxy server where a shared history link can be generated (including Galaxy Main https://usegalaxy.org), you can post it back here (publically) or send it to me as a direct message (private), and we can help to troubleshoot.

Should you be doing something else (different tool, etc), please explain with more details.

Thanks!

We did the following:

Select lines that match an expression --> get flanks --> extract genomic DNA using coordinates from assembled/unassembled genomes and lastly sequence logo generator for fasta

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Thanks for the extra info.

The Sequence Logo tool requires a fasta input that is in an alignment format, not just a regular fasta file. ClustalW can be used to generate the proper fasta input – use the output option “Output alignment format” as “fasta”.

Please be aware that ClustalW does have some input limitations on the public server, so do not submit too many fasta sequences at once or that tool will fail. How many exactly depends somewhat on the length of the input fasta sequences, so you’ll need to test what works for your data if > 100 sequences or so.

I’ll also go in and run a test with some sample data to make sure there is not more going on and will write back with that result. I am also going to test MAFFT (potential alternative tool for ClustalW step) – cannot recall if the aligned fasta produced by that tool works with Sequence Logo or not.

Please try ClustalW in the meantime and see if that works for you.

Okay great! I will do so

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Update: Both ClustalW and Mafft will produce the correct aligned fasta format for Sequence Logo. (What I expected but wanted to confirm).

You can try one or both and decide which you prefer. Mafft has more tool settings you can experiment with if ClustalW fails for memory resources (before reducing the input size).

Its working! Thank you so much!

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Great news! :smile:

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