User: yelekley7

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yelekley70
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Posts by yelekley7

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variable regions within exons of a gene
... Hello, Could someone please suggest where to find a list of variable regions (snps) within exons of a specific human gene located on chromosome six? I can locate the gene in ncbi and Ensemble but I'm not sure how to locate the SNPs. Which tools databases would be appropriate? Thank you very much f ...
gene written 11 days ago by yelekley70 • updated 10 days ago by Denise - Open Targets3.9k
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how to distinguish between artifacts and real indels?
... Hello, I’m working with multiple sequences (fasta format) of the same human gene (exons 2,3,4). Each sequence is about 5300 nucleotides long. When I import the sequences into MEGA I can see that there are multiple “-“ deletions and “|” insertions in random places. These sequences came from a sof ...
alignment written 4 months ago by yelekley70
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Comment: C: Errors when re-importing an alignment back to Mega
... I ran the alignment today and clicked on "Data/Phylogenetic Analysis". It opened a Text file editor and displayed an error message "Invalid base found" and it goes to the end on the alignment were there are no bases. This happens even before I export the data. The same error occurs when I import t ...
written 4 months ago by yelekley70
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Errors when re-importing an alignment back to Mega
... Hello, I would really appreciate if someone could advise on the following error with Mega7 GUI version. I'm experiencing errors when trying to re-import alignments back into Mega. I performed ClustalW alignment on 400 protein sequences and exported in .meg format. However, when I try to open the ...
software error alignment written 4 months ago by yelekley70
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Comment: C: convert fasta dna files to protein
... MEGA is cool, thanks ...
written 4 months ago by yelekley70
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Comment: C: convert fasta dna files to protein
... Do you use SnapGene viewer or snagene_2.0 that charges fees? Is there free software that would allow to import aligned protein sequences, align them to a reference and mark them up? Thanks ...
written 4 months ago by yelekley70
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Comment: C: convert fasta dna files to protein
... I was able to get ESPript to output a result after I trancated the aligned protein seqences. However, it did not correctly predict the location of the six epitopes within the 6 aligned sequences. Perhaps, if I upload more sequences the prediction will be more accurate? I'm a little disappointed bu ...
written 4 months ago by yelekley70
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Comment: C: convert fasta dna files to protein
... I'm trying out the ESPript tool. I've ran Clustal Omega and saved the alingnment output in a Note Pad with .aln extension. I've uploded the file into "Aligned Sequence" tab and it looks like it's running but there is no indication weather it's working or when it will finish. How long does it usually ...
written 4 months ago by yelekley70
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Comment: C: convert fasta dna files to protein
... ExPaSy output generates multiple frames (3) and provided 5'3' and 3'5 for each. Do I need to select a particular frame and 5'3'/3'5' sequence to upload into Clustal Omega. All sequences should be in the same frame since they represent different alleles of the same gene. Perhaps I'm wrong? Also, I c ...
written 4 months ago by yelekley70
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Comment: C: convert fasta dna files to protein
... 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 ran cat *.fas > output.txt to combine multiple f ...
written 4 months ago by yelekley70

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