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  • GenoMax
    replied
    Originally posted by HLAgroupLK View Post
    I've also tried ExPasy tool and it generated an output on the screen but it's not clear to me how to download the result. Also, my final goal is to import the result into Culstal Omega to do the alignment so the format of the output has to be compatible. Should I stick with ExPasy?

    Thanks
    Option 1: Highlight and copy/paste the result data into a separate text file (I assume result is already in fasta format). Be sure to save the file in text format.

    Option 2: Choose "file" --> "Save Page as" from your browser window. Be sure to select format as "text file" for the file being saved.

    First option may be cleaner. You can then open the file in MEGA or upload to Clustal Omega.

    Leave a comment:


  • HLAgroupLK
    replied
    So far, I've tried EMBOS Transeq and the run aborted before generating anyting for some reason. I've combined multiple fasta files (size was under 1 MB). It worked when I tried it with a really small fasta file. I'm not sure what the problem is?

    I've also tried ExPasy tool and it generated an output on the screen but it's not clear to me how to download the result. Also, my final goal is to import the result into Culstal Omega to do the alignment so the format of the output has to be compatible. Should I stick with ExPasy?

    Thanks

    Leave a comment:


  • GenoMax
    replied
    Cross-posted: https://www.biostars.org/p/239422/

    Has been answered there.

    Leave a comment:


  • Brian Bushnell
    replied
    I've also written a nifty tool for nucleotide -> amino translation, but that does not appear to be the goal in this case. Rather, it appears that there are multiple small sequences in a 5500bp region that need to be translated with correct frames. To do so, you need to know the boundaries of these short peptide-encoding sequences, and ignore the non-coding sequence. I don't know of a tool which does that.

    Leave a comment:


  • gringer
    replied
    I've used transeq from the EMBOSS suite:



    There's a command-line version as well, as part of the free EMBOSS toolkit that is available in most Linux distributions:

    EMBOSS, European Molecular Biology Open Source Software Suite, bioinformatics, EBI, European Bioinformatics Institute, Molecular Biology, Computational Biology, Open Source, Software, Database

    Leave a comment:


  • HLAgroupLK
    started a topic converting fasta dna files to protein

    converting fasta dna files to protein

    Hello,

    I have 200 human fasta dna files from a region of chr6. Each sequence is 5,500 bp each. I've combined these fasta files and uploaded them into Clustal Omega to generate multiple sequence alignments and phylogenetic tree.

    It worked well, however, I would like to convert these sequences into protein and highlights epitopes present in the sequences. What is the best tool to used for this purpose? What format do I need to select for the output?

    Thank you so much for your advice.

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  • seqadmin
    Recent Advances in Sequencing Analysis Tools
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    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
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