User: l.souza

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l.souza70
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Brasilia, Brazil
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5 months, 4 weeks ago
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2 years, 6 months ago
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Posts by l.souza

<prev • 87 results • page 1 of 9 • next >
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Comment: C: Primer design for specific organism
... Tools for primer design is not regarding Bioinformatics? The inserted gene is just the CDS... It is not 100 % identical with the endogenous one; however, all primers I've designed with Primer3 also hit in the endogenous one. ...
written 8 months ago by l.souza70
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Primer design for specific organism
... Hello everyone, I have an exogenous gene inserted in a plant to quantify via RT-qPCR. However, the transformed plant also has an endoogenous copy of this gene. Is there a way to design a pair of primers for the exogenous gene without binding to the endogenous one? At Primer-BLAST there's an option ...
gene primer rt-qpcr written 8 months ago by l.souza70
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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 9 months 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 9 months ago by l.souza70 • updated 9 months ago by Bill Pearson860
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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 9 months 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 9 months 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 23 months ago by l.souza70 • updated 23 months ago by genomax75k
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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 2.2 years 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 2.2 years ago by l.souza70 • updated 2.2 years ago by Joe15k
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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 2.3 years ago by l.souza70

Latest awards to l.souza

Popular Question 6 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 Publication-Quality Multiple Sequence Alignment
Popular Question 14 months ago, created a question with more than 1,000 views. For Publication-Quality Multiple Sequence Alignment
Popular Question 14 months ago, created a question with more than 1,000 views. For Software for Tree Visualization
Popular Question 14 months ago, created a question with more than 1,000 views. For Nucleotide statistics for fasta sequences
Popular Question 14 months ago, created a question with more than 1,000 views. For Extracting information from a genbank file
Popular Question 16 months ago, created a question with more than 1,000 views. For Extracting information from a genbank file
Popular Question 16 months ago, created a question with more than 1,000 views. For Software for Tree Visualization
Scholar 2.4 years ago, created an answer that has been accepted. For A: DNA sequences trimming methods
Rising Star 2.5 years ago, created 50 posts within first three months of joining.
Scholar 2.5 years ago, created an answer that has been accepted. For A: DNA sequences trimming methods
Supporter 2.5 years ago, voted at least 25 times.
Scholar 2.5 years ago, created an answer that has been accepted. For A: DNA sequences trimming methods
Scholar 2.5 years ago, created an answer that has been accepted. For A: DNA sequences trimming methods

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