User: l.souza

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l.souza70
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70
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Location:
Brasilia, Brazil
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3 days, 8 hours ago
Joined:
1 year, 10 months ago
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l***************@outlook.com

Posts by l.souza

<prev • 85 results • page 1 of 9 • next >
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Answer: A: Tools for qRT-PCR data analysis
... This is the usual RT-qPCR analysis workflow I use: 1. Retrieve the Rn values and input at [Miner][1] to get CTs, reaction efficiency and some statistics; 2. Load the Miner info into [REST 2009][2] withou choosing the reference genes; 3. Load the preliminar results into [geNorm][3] to pick up the ...
written 13 days ago by l.souza70
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What kind of BLAST to use in Gene Ontology?
... Hello everyone, I am performing a Gene Ontology analysis with the proteins obtained by a Proteomics experiment. To achieve the gene ontology I choose to use Blast2GO; however, I got a doubt regarding using blastp or tblastn in this analysis. When using tblastn, I got hits with species pretty dista ...
alignment protein gene ontology blast written 13 days ago by l.souza70 • updated 13 days ago by Bill Pearson850
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Error when running sma3s for proteome annotation
... Hello everyone, I have been trying to run sma3s for protein annotation, according to the author's instructions (UPOBioinfo Group). However, when running the command ./sma3s.pl -i query_dataset.fasta -d uniref90.fasta -goslim I got the message *"Problem with blastdbcmd. It could be due to an ...
annotation proteome go sma3s written 16 days ago by l.souza70
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How to match proteins to a genome
... I would like to map the identified proteins obtained by a LC-MS/MS experiment to an existing genome sequence deposited at PATRIC database. I have a list with the proteins accession (Uniprot). Does anyone have a suggestion on how to do it? Best regards, Lucas ...
proteomics patric genomics written 22 days ago by l.souza70
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How to divide FASTA file?
... Hello! I have a FASTA file with about 1600 sequences. But, I'm gonna use a tool that requires the FASTA files possess up to 200 sequences. Is there a way to automate the division of this file using Linux or Windows? Thanks in advance. ...
fasta sequences written 14 months ago by l.souza70 • updated 14 months ago by genomax63k
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Comment: C: RSMD in homology modelling protein
... The TM-score is 0.64319. So, according to the reference value, the protein is in about the same fold, right? Visually, they seem to be well imposed, with isolated places not so good (most of them are presented as coil). ...
written 17 months ago by l.souza70
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RSMD in homology modelling protein
... Hello everyone, I am modeling a protein through homology approach. My protein has a large disordered structure (~46% of coil). After the refinement, the RSMD between the template and the final model was 3.68Å. Is it too high? Thanks in advance! ...
protien rsmd homology written 17 months ago by l.souza70 • updated 17 months ago by jrj.healey11k
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Comment: C: Why to delete gaps in alignments to phylogeny?
... Thank you, Jean-Karim! Would you say that trimAl is trustworthy? ...
written 19 months ago by l.souza70
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Why to delete gaps in alignments to phylogeny?
... Hello, everybody! I've been reading the chapter 3 of *The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing* by Des Higgins and Philippe Lemey, that talks about multiple sequence alignment to phylogenetic approaches. And the authors suggest deleting gap r ...
phylogeny gaps sequences written 19 months ago by l.souza70 • updated 19 months ago by Jean-Karim Heriche18k
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Comment: C: What is a good tool to make saturation analyses?
... I'm talking about mutation saturation ...
written 19 months ago by l.souza70

Latest awards to l.souza

Popular Question 5 months ago, created a question with more than 1,000 views. For Publication-Quality Multiple Sequence Alignment
Popular Question 5 months ago, created a question with more than 1,000 views. For Software for Tree Visualization
Popular Question 5 months ago, created a question with more than 1,000 views. For Nucleotide statistics for fasta sequences
Popular Question 5 months ago, created a question with more than 1,000 views. For Extracting information from a genbank file
Popular Question 7 months ago, created a question with more than 1,000 views. For Extracting information from a genbank file
Popular Question 7 months ago, created a question with more than 1,000 views. For Software for Tree Visualization
Scholar 20 months ago, created an answer that has been accepted. For A: DNA sequences trimming methods
Rising Star 21 months ago, created 50 posts within first three months of joining.
Scholar 21 months ago, created an answer that has been accepted. For A: DNA sequences trimming methods
Supporter 21 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: DNA sequences trimming methods
Scholar 21 months ago, created an answer that has been accepted. For A: DNA sequences trimming methods

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