User: n00bgenome

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n00bgenome20
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Posts by n00bgenome

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Comment: C: Clustering protein sequences
... I also made a max likelihood tree and got much the same result. I want to find a few sequences that will have enough 'coverage' of the diversity of all the sequences. So if I chose 10 clusters, and I picked a representative sequence for each cluster, than I would have a high level of similarity in ...
written 3.8 years ago by n00bgenome20
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Comment: C: Clustering protein sequences
... Here is what the NJ tree did: http://postimg.org/image/ciq2ckjox/ So the problem is that I don't have any sense of how far away those clusters in the trees are. It seems like protdist might be the way to go to get that information? Can you recommend how I'd go about doing that, in slightly more de ...
written 3.8 years ago by n00bgenome20
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Comment: C: Troubleshooting MCL - always returns 1 cluster no matter inflation value
... ![Neighbor joined tree][1] http://postimg.org/image/ciq2ckjox/ There is a neighbor joined tree of the data. Its very frustrating that I can't get MCL to work with it. These were the commands I used: **BLAST** makeblastdb -in K02405.65.fa -dbtype prot -out K02405.65DB blastp -query K02405.65.fa - ...
written 3.8 years ago by n00bgenome20
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Comment: C: Clustering protein sequences
... They are definitely not all unique, if anything, they are too similar. My blast results show *the vast majority of E values above E-10. I don't want to cluster them into definitively 10, but they should be able to be grouped further. MCL just gives me 1 cluster as if they are all too similar to be p ...
written 3.8 years ago by n00bgenome20
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Clustering protein sequences
... Hi all, What I'm trying to do is take a large number of amino acid sequences (~1000) and condense them to a few clusters (~10), based solely on similarity of the sequences. These amino acid sequences are all orthologs to begin with (same Pfam family). I have taken two approaches for this, and I am ...
mcl protdist seqboot phylip clustering written 3.8 years ago by n00bgenome20 • updated 3.8 years ago by Biostar ♦♦ 20
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Troubleshooting MCL - always returns 1 cluster no matter inflation value
... Hello, I am trying to use MCL to cluster together a group of sequences. I am following this protocol http://micans.org/mcl/ I first took my ~1000 sequences and ran CD-Hit, and I used the Cluster65 file, which reduced total number of clusters to 164. I then did a blastp all-against-all and I used t ...
clustering written 3.8 years ago by n00bgenome20
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Comment: C: Meaningful clusters in phylogenetic trees
... Oh, I think I understand now. I should do a Muscle MSA after the CD-HIT, and then use those sequences to do Blast. These sequences should first be made into a database with makeblastdb and then Blasted all against all using blastp (why not blastall -p blastp?). I can then submit this to MCL. Is that ...
written 3.8 years ago by n00bgenome20
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Comment: C: Meaningful clusters in phylogenetic trees
... Is blastP inferior to Muscle? I could either do k-means clustering or MCL, and I think MCL would give me what I want, but it only takes in blast files. After reading more, I have realized I am interested in phenetic differences, not phylogeny. ...
written 3.8 years ago by n00bgenome20
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Answer: A: Meaningful clusters in phylogenetic trees
... Thanks so much! cd-hit gets rid of many of the redundant species. I meant to ask a new question in a different thread now, but I've unintentionally "answered" here, so I thought it would be better to ask my next question than to post another thread. So I'd like to take my file of sequences and do ...
written 3.8 years ago by n00bgenome20
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Answer: A: Meaningful clusters in phylogenetic trees
... I think I have a partial answer based on the following question: https://www.biostars.org/p/6910/ Fundamentally, my question is if one has hundreds or thousands of sequences that have been aligned, how does one group them together based on sequence similarity into a tree or clusters based on sequ ...
written 3.8 years ago by n00bgenome20

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