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Q&A Report From The Workshop - Exploring EMBL-EBI Sequence Analysis Tools and Managing Bioinformatics Workflows

The Q&A report from the workshop contained questions about multiple sequence alignment tools, submitting sequences for alignment, supported file formats, sequence number and size limits, the meaning of e-value in BLAST, and examples of standard protein sequences. Answers indicated that the best tool depends on the input sequences, Clustal Omega and ClustalW are different MSA programs, sequences can be pasted into the input box, common alignment formats include FASTA, Clustal, Stockholm, and there are limits on sequence numbers and sizes due to file size restrictions.

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Zakaria Kasmi
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63 views4 pages

Q&A Report From The Workshop - Exploring EMBL-EBI Sequence Analysis Tools and Managing Bioinformatics Workflows

The Q&A report from the workshop contained questions about multiple sequence alignment tools, submitting sequences for alignment, supported file formats, sequence number and size limits, the meaning of e-value in BLAST, and examples of standard protein sequences. Answers indicated that the best tool depends on the input sequences, Clustal Omega and ClustalW are different MSA programs, sequences can be pasted into the input box, common alignment formats include FASTA, Clustal, Stockholm, and there are limits on sequence numbers and sizes due to file size restrictions.

Uploaded by

Zakaria Kasmi
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as XLSX, PDF, TXT or read online on Scribd
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Q&A Report from the workshop:

Question
What is the best msa tool?

clustal 2 and clustal omega are the same


How would we enter multiple sequences? because there is only one input box
Could the legend explaining symbiols (*, -,...) be shown in the result window?
What is the max number of sequences one can upload?
Is there a limit on the number of sequences or the size of the file that I submit to Clustal O
Is there a best tool when it comes to the MSA ?
other than fasta what file formats are used for alignment
The Sequence provided for BLAST , is that FASTA ? he NCBI BLAST tool (Nucleotide BLAST) co
can you please tell me a some standard protein to work with pdb database just to understan
What does ENA stand for? (ENA Coding; ENA Geoespacial, etc, under Database)
I tried using the EMBOSS needle tool for pairwise alignment using nucleotide sequence. Howev
What is e-value in BLAST?
Please kindly share the python webiner
Does your server support large dataset analysis using code or command line? or we need to
Exploring EMBL-EBI sequence analysis tools and managing bioinformatics workflows
Answer
It is difficult to say because different tools will do better under different scenarios - i.e. depends on the input seque
The best is to try multiple and change some parameters to see if the result is somewhat consistent, which would gi
Clustal Omega and ClustalW are different programs used for Multiple Sequence Alignment.
You need to copy & paste multiple sequences into the input box. Click on the example sequence to get a fill off wha
* indicates positions which have a single, fully conserved residue.
We have file size limit which corresponds to up to a few thousand sequences (depends on the sequence length).
We have file size limit which corresponds to up to a few thousand sequences (depends on the sequence length).
It is difficult to say because different tools will do better under different scenarios - i.e. depends on the input seque
We have a list of example sequence formats: https://www.ebi.ac.uk/jdispatcher/docs/formats/
The MSA
Sorry, yes outputs
the inputare usually
is in fasta in ClustalEither
format. Format, MSF,
there is aStockholm,
problem withetc.the input format or could be a bug in our appli
You could probably try using this example: https://www.ebi.ac.uk/pdbe/pdbe-kb/proteins/Q14676/structures
European Nucleotide Archive - https://www.ebi.ac.uk/ena/browser/home
HI,
Maybe you can
Expectation tryIts
Value, anya local alignment
statistical measuretools.
how Worth
likelychecking if there
you are to is any
find that specialised
alignment tool though
by chance.
https://www.ebi.ac.uk/training/events/programmatic-access-uniprot-using-python-2023/
We only support running a selection of locally installed bioinformatics applications. For exploratory analysis usin
epends on the input sequences and the complexity of those sequences.
consistent, which would give you better confidence about the result.

equence to get a fill off what I mean.

on the sequence length).


on the sequence length).
epends on the input sequences and the complexity of those sequences.

could be a bug in our application. IF you are confident your input is well formatted please send us a ticket (via feedback button
ns/Q14676/structures

ool though

exploratory analysis usin


cket (via feedback button) so we will investigate it for you.

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