User: sentausa

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sentausa610
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sentausa
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Posts by sentausa

<prev • 109 results • page 1 of 11 • next >
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Comment: C: MAUVE - genome alignment
... What do you mean with orthologous "clusters"? Orthologous genes? You can use other tools like OrthoMCL, [Proteinortho][1], or [OrthoFinder][2] to find orthologous genes between genomes, and it's more effective than using Mauve. [1]: https://www.bioinf.uni-leipzig.de/Software/proteinortho/ [2]: ...
written 11 months ago by sentausa610
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Comment: C: MAUVE - genome alignment
... And why do you want to detect orthologs which are common between the genomes? What do you mean by orthologs here? Orthologous genes? And if you have them, what will you do to them? I just want to know what you really want to do so that I can help you, not necessarily using Mauve. ...
written 11 months ago by sentausa610
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Comment: C: Making RefSeq in Windows
... I don't understand your question. What do you mean adding "your" track to "this" list? Which track? What list? And by the way, a reference genome track should have a similar icon to a sequence (fasta, genbank) file, that is a red horizontal double helix, but with 3 small blue vertical stripes under ...
written 11 months ago by sentausa610
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Comment: C: protein identification in proteome file using bioinformatics tools
... What do you mean with a proteome file? Amino acid sequences? Mass spectrometry data? ...
written 11 months ago by sentausa610
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Comment: C: MAUVE - genome alignment
... What exactly do you want to get? What do you mean by saying that you "want to find the orthologus regions which are present in these genomes"? I'm sensing that you're not doing the correct approach by using Mauve. ...
written 11 months ago by sentausa610
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Comment: C: Making RefSeq in Windows
... My previous comment was to tell you how to convert a fasta file of the genome to a reference track. Your question from the beginning was how to have this reference genome, right? As I've mentioned, just tick "Create sequence track" and ignore (un-tick) CDS, gene, transcripts, etc. The result is a re ...
written 11 months ago by sentausa610
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Comment: C: Making RefSeq in Windows
... You mean how to convert a fasta file to track? Here is the manual: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Convert_tracks.html. So, for example, if you already have the fasta file of E coli ST131 genome imported to CLC, right click on it, Toolb ...
written 11 months ago by sentausa610
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Comment: C: Making RefSeq in Windows
... In that case (option 2 in my link), you can simply convert the fasta/genbank file of the genome of interest (e.g. E coli ST131) to a track, which will be called "something (genome)", and then use the resulting track as the reference genome track. ...
written 11 months ago by sentausa610
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Comment: C: Making RefSeq in Windows
... I really don't understand why you need to make a custom track. Have you seen the manual on tracks? http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Retrieving_reference_data_tracks.html ...
written 11 months ago by sentausa610
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Comment: C: Making RefSeq in Windows
... Have you tried with a genbank file? This is the link to the genbank entry of E coli ST131: http://www.ncbi.nlm.nih.gov/nuccore/HG941718.1. You can download the genbank file and convert it to tracks on CLC. ...
written 11 months ago by sentausa610

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