User: peifei0418

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peifei04180
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Posts by peifei0418

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Comment: C: Does ambiguous nucleotides affect analysis?
... Sequence analysis here involved coronavirus genome sequence analysis. I did multiple sequence alignment of the human coronaviruses and I saw there is a lot of ambiguous nucleotides in the alignment. The MSA done as a step for comparative genome analysis to compare human CoVs genomes and find the eff ...
written 15 days ago by peifei04180
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Does ambiguous nucleotides affect analysis?
... Hi guys, if there are some ambiguous nucleotides appear in your sequences, does it affect the sequence analysis in general? Usually researchers will remove ambiguous nucleotides because they produce noise and affect analysis, is it correct? Or are there any importance of ambiguous nucleotides that ...
ambiguousnucleotides written 17 days ago by peifei04180 • updated 17 days ago by Joe18k
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Comment: C: Problem with MAFFT Multiple Sequence Alignment
... Hi there, I have tried MAFFT online server but my sequence data are too big to run in MAFFT server. My job get killed when I tried in MAFFT server due to time restriction. MAFFT online server only allows users' MSA job to run for 24 hours. After 24 hours the server will automatically terminate your ...
written 4 weeks ago by peifei04180
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Problem with MAFFT Multiple Sequence Alignment
... Hi guys, I ran MSA with MAFFT (FFT-NS-i method with two cycles) in my university server, which has 31.3GB memory and 31.9GB swap memory. My input file has 8579 sequences (All human coronaviruses) [~253MB]. The job has running for 5 days already and suddenly the job has been killed not long ago (afte ...
genome alignment msa error mafft written 4 weeks ago by peifei04180 • updated 4 weeks ago by Mensur Dlakic8.2k
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Comment: C: Multiple Sequence Alignment Tool for Large Dataset
... Oh I see, thank you for the suggestions and explanations. Unfortunately, the special option provided by MAFFT only applied for SARS-CoV-2 genomes that are very closely related (~95% identity). My sequences contain other human coronaviruses as well so this special option is not suitable for my data ...
written 6 weeks ago by peifei04180
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Multiple Sequence Alignment Tool for Large Dataset
... Hi everyone, I'm currently planning to run MSA on all human coronaviruses. I have 8,586 complete genomes/sequences and the FASTA file size is around ~256MB. May I ask does MAFFT can accept this number of sequences as input? I heard about MUSCLE and T-Coffee before and their accuracy are quite okay, ...
genome alignment sequence coronavirus written 7 weeks ago by peifei04180 • updated 7 weeks ago by Mensur Dlakic8.2k
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Comment: C: Comparative Genome Analysis vs. Comparative Genomics
... Thank you so much for sharing these links and all of them are informative, really appreciate it a lot! ...
written 7 weeks ago by peifei04180
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Comment: C: Does the host of human coronaviruses (CoVs) genomes/sequences must be from human
... Oh I see, I have understood. Thank you for the explanations, it helps me a lot! :) ...
written 8 weeks ago by peifei04180
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Comment: C: Comparative Genome Analysis vs. Comparative Genomics
... Oh I see. Thank you for the explanations. :) May I know which tools they will be using to search for conserved sites and indels? Because this is the thing I'm searching for my project, and it's quite hard to find as some articles did not stated about this at all (tools or techniques they used to sea ...
written 8 weeks ago by peifei04180
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Comment: C: Does the host of human coronaviruses (CoVs) genomes/sequences must be from human
... Yes, I knew SARS-CoV is originated in bats as well. Thank you for the suggestion about posting on biology stackexchange. I will try to post this in other forum. Thanks a lot for the response, really appreciate it. Hope you have a good day ahead :)) ...
written 8 weeks ago by peifei04180

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