User: satanicodr

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satanicodr100
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Posts by satanicodr

<prev • 10 results • page 1 of 1 • next >
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Answer: A: hmmpress error with a hmm database
... I found the answer elsewhere. To solve this issue you need to convert the different versions of the individual hmms to the most recent version using hmmconvert. hmmconvert > Then you can concatenate and press the database. for i in `ls *hmm | sed 's/.hmm//g'`; do hmmconvert ${i}. ...
written 13 months ago by satanicodr100
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Answer: A: 16S rRNA alignment
... The 16S rRNA molecule has secondary structure and an aligner that does not consider this is not good for phylogeny. If you want to find its closest relative just go to a specialized database such as the Ribosomal database project or the Silva database. There you will be able to find all related sequ ...
written 22 months ago by satanicodr100
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Answer: A: How to find chromosome coordinates based on gene locus
... Go to http://www.ncbi.nlm.nih.gov/genome/proteins/4?genome_assembly_id=22492&gi=240254421 And look for the genes or download the annotation tables for all the chromosomes and then do a search on them,      ...
written 22 months ago by satanicodr100
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Comment: C: blastn output and methods to quantify similarities between sequences
... Blast is not the right tool because there is a limit on how many sequences it will report. In theory you could make one database for each sequences or divide the sequences into many small groups and then run blast for each sequence against that database but that would be inefficient. A more efficie ...
written 22 months ago by satanicodr100
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Answer: A: blastn output and methods to quantify similarities between sequences
... What you really want is to align all your sequences together and create a huge distance matrix (100k x 100k). Then you can use this matrix to do a clustering analysis to see how many groups you have at a defined level of similarity. Alternatively you can use a greedy algorithm such as cd-hit that wi ...
written 22 months ago by satanicodr100
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Answer: A: Fastx Clipper Not Accurate In Adapter Clipping For 100Nt Reads
... I recently compared the different programs to remove adaptors (illumina) for 75bp and 150 bp reads and trimmomatic performed the best for me. I measured performance with FASTQC and considered the ability of the programs to run in parallel. I compared fastx, trimmomatic and NGSQCToolkit_v2.3. this i ...
written 4.4 years ago by satanicodr100
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Answer: A: Why Is Maximum Likelihood Thought To Be The Best Way To Build Phylogenetic Tree?
... There are some paper that actually compare performance of different algorithms. the one below showed that ML and Bayesian trees algorithm outperform NJ, and MP one in accuracy, and there are some factor such as branch length, and neighbor branch length affect the accuracy. Ogden, T.H., and M.S. Ros ...
written 4.4 years ago by satanicodr100
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Answer: A: How Does One Decide Which Bacterial Taxonomic Classification To Use: Rdp, Silva
... RDP uses the Bergeys taxonomy, which is more conservative and standard. Silva and Greengenes use their own taxonomies which are developed by their own teams and collaborators. For some groups, collaborations have improved the taxonomy and may help you if you are working with a specific groups of org ...
written 4.5 years ago by satanicodr100
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Answer: A: Closest Related Bacterial Species
... For the closes relative you can try using a 16S rRNA database such as the Ribosomal Database Project, Silva or Greengenes. In RDP you can use the seqmatch function. For some groups, 16S may not provide the best resolution so you will have to use another gene such as recA or rpoN, For even better re ...
written 5.0 years ago by satanicodr100
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Answer: A: Downloading 16S Sequences From Rdp And Greengenes
... For the RDP. 1. Go to the website and click on "Browser": 2. Change the options if you want to include shorter sequences or low quality ones and click on "browse" 3. Click on "+" left to Bacteria if you want all the bacterial sequences, do the same for other groups if you are interested 4. Click on ...
written 5.2 years ago by satanicodr100

Latest awards to satanicodr

Supporter 12 months ago, voted at least 25 times.
Scholar 22 months ago, created an answer that has been accepted. For A: How to find chromosome coordinates based on gene locus
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: How Does One Decide Which Bacterial Taxonomic Classification To Use: Rdp, Silva

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