User: Raquel Tobes

gravatar for Raquel Tobes
Raquel Tobes140
Reputation:
140
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Trusted
Location:
Spain
Website:
http://www.era7bioinfo...
Last seen:
2 years, 6 months ago
Joined:
6 years, 10 months ago
Email:
r*****@era7.com

Bioinformatician. Bacterial genomics. NGS.

Posts by Raquel Tobes

<prev • 13 results • page 1 of 2 • next >
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Meaning of the results of Music Survival program
... Following the documentation about survival program (integrated in Music suite) available at: http://gmt.genome.wustl.edu/packages/genome-music/genome-music-survival.html  I understand that the analyses include the Kaplan-Meier estimator followed by the Cox Proportional Hazards model but I am not co ...
music written 2.7 years ago by Raquel Tobes140 • updated 2.6 years ago by Biostar ♦♦ 20
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Answer: A: How Do Researchers Choose A Reference Genome For A Novel Bacterial Strain Assemb
... I think that, for bacterial genomes, de novo assembly is always better since the assembly using a reference genome inevitably causes bias to the reference genome. ...
written 5.6 years ago by Raquel Tobes140
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Comment: C: Measuring Conservation
... There are a lot of important papers about evolutionary questions, including horizontal gene transfer, based on protein similarity because nucleotide sequence similarity implies protein similarity but the analysis of nucleotide sequences adds additional features (codon usage, k-tuple frequencies, GC ...
written 5.6 years ago by Raquel Tobes140
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Answer: A: Measuring Conservation
... Firstly, you can analyze conservation between nucleotide sequences or between protein sequences. Analyzing protein conservation you are mainly focused to functional constraints while nucleotide sequences maintain traceable some features related with their evolutionary origin. It’s also interesting t ...
written 5.6 years ago by Raquel Tobes140
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Answer: A: Best Way To Close Gaps In Genome With Single Reads
... PacBio long reads sequencing, even with low coverage, could be a good solution for scaffolding if you have a de novo initial assembly of a bacterial genome by example. ...
written 5.6 years ago by Raquel Tobes140
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Answer: A: Problematic Representantive Members Found In Uniref 100/90/50 Xml Files
... In this Uniprot page (http://www.uniprot.org/help/uniref) you can find this information: "In addition to UniProtKB records, UniRef100 also includes the UniParc entries that are not covered by UniProtKB and contain cross-references to the following databases: •Ensembl Chicken •Ensembl Cow •Ensembl Do ...
written 6.0 years ago by Raquel Tobes140
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Comment: C: How To Find Paralogs Using Blast
... Could you include here an example in which the score of a putative paralog vs Protein 1 is higher than the score of the Protein 1 vs Protein 1? Thanks ...
written 6.3 years ago by Raquel Tobes140
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Answer: A: How To Find Paralogs Using Blast
... To consider the score obtained in the alignment to itself as the reference could be a good option. Each protein aligned to itself obtains in BLAST an specific score. To know if the similarity is sufficiently significant to consider the two aligned proteins as paralogs it would be more precise if y ...
written 6.3 years ago by Raquel Tobes140
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Comment: C: Query Vs. Target Using Blast2
... In addition perhaps the position of the similarity region could be more advantageous in a specific case. If the similarity region is placed at the end of the query could be easily detectable as query (it is only a possibility) ...
written 6.5 years ago by Raquel Tobes140
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Comment: C: Query Vs. Target Using Blast2
... With regard to the asymemtry the algorithm implies that the results are different if you interchange target by query. The initial step of BLAST algorithm is to create a deterministic finite state machine to search all words of a size W that are over a similarity threshold with any word of the query ...
written 6.5 years ago by Raquel Tobes140

Latest awards to Raquel Tobes

Supporter 5.5 years ago, voted at least 25 times.
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: How Do Researchers Choose A Reference Genome For A Novel Bacterial Strain Assemb
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Measuring Conservation
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Problematic Representantive Members Found In Uniref 100/90/50 Xml Files

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