User: brittanymlebert

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Posts by brittanymlebert

<prev • 9 results • page 1 of 1 • next >
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PorthoMCL for Ortholog Clustering
... I am trying to run Orthologous clustering on a set of 20 genomes for comparative genomics. I found the program PorthoMCL, which is supposed to be an easier and faster alternative to OrthoMCL. I uploaded my 20 protein fasta files and the program ran very quickly. However, the output is very confusing ...
orthologous clustering written 12 days ago by brittanymlebert10
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Comment: C: Running Blastall Before MCL for Paralog Clustering
... Thank you so much! Your reply was very helpful! ...
written 12 days ago by brittanymlebert10
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Comment: C: Running Blastall Before MCL for Paralog Clustering
... Thank you for your response! It was not working because of how I formulated the command. Do I run each of the 13 protein fasta files separately? And also, what database am I supposed to be blasting them to in order to run MCL? ...
written 17 days ago by brittanymlebert10
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Running Blastall Before MCL for Paralog Clustering
... Hello, I am trying to use MCL to do paralog clustering of 13 genomes for comparative genomics. I have been using the protocol "Using MCL to Extract Clusters from Networks" as a reference for doing this. In the protocol, it says that I have to run `blastall -p blastp` with the `-m8` parameter on my ...
mcl comparative genomics blast written 18 days ago by brittanymlebert10 • updated 18 days ago by Mensur Dlakic5.5k
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InterPro Names from ID (Blast2Go)
... Hello, I ran functional annotations on a genome using InterProScan through Blast2Go. However, the output only shows the InterPro IDs instead of the actual names of the Pfams. How can I efficiently get the InterPro names without having to search each of the IDs separately? I have looked online and h ...
genome written 7 weeks ago by brittanymlebert10
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Comment: C: Functional Annotations After GeneMark-ES
... I actually found a way to just download the translated sequences from Geneious, which was really easy. Thank you for all of your help. I really appreciate it! ...
written 9 weeks ago by brittanymlebert10
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Comment: C: Functional Annotations After GeneMark-ES
... Thank you very much! I understand now. I have been researching a simple way to just get a fasta of the protein translations from a genomic sequence fasta and a .gtf file. Do you have any suggestions? ...
written 9 weeks ago by brittanymlebert10
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Comment: C: Functional Annotations After GeneMark-ES
... Thank you for your response! I see what you mean about the combination of the fasta and the .gtf, as there are now automatic translations on Geneious under my sequences. What I'm still confused about it what file I put into Blast2Go, because it is just asking for a fasta file of actual sequences. Wh ...
written 9 weeks ago by brittanymlebert10
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Functional Annotations After GeneMark-ES
... This may be a stupid question, but I am very new to bioinformatics. I am trying to annotate a novel fungal genome. I just ran it through GeneMark-ES to annotate it and got a .gtf output. When I put this file into Geneious it attaches to my FASTA file and shows me all of the introns and exons on the ...
genome written 9 weeks ago by brittanymlebert10 • updated 9 weeks ago by lieven.sterck7.9k

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