User: lgbi

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lgbi150
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Posts by lgbi

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Comment: C: 454 Sequences: Lower Case Base Call In Reverse Primer
... I'm using the sffinfo tool provided by Roche. ...
written 6.3 years ago by lgbi150
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454 Sequences: Lower Case Base Call In Reverse Primer
... After converting a 454 SFF file to FASTQ, I get sequences like this: tcagAGTACGCTATGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTATAACCACTCAAGCTCTCGCTTGGTATTGGGGCTCGCGGTTTCGCGGCTCCTAAAATCAGTGGCGGTGCCTATCGGCTCTACGCGTAGTAATACTCCTCGCGATTGAGTCCGGTAGGTCTACTTGCCAGCAACCCCTAATTTT ...
454 written 6.3 years ago by lgbi150 • updated 3.6 years ago by Biostar ♦♦ 20
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Running Blastn Locally: Exclude Uncultured Sequences
... When running BLAST throught the NCBI web interface, one can check the "exclude uncultured sequences" checkbox. When I run blast with BioPython on NCBI, I can add the Entrez query "all [filter] NOT(environmental samples[organism] OR metagenomes[orgn])" to obtain the same. Now I've downloaded the nt ...
blastn written 6.7 years ago by lgbi150 • updated 4.7 years ago by Biostar ♦♦ 20
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Answer: A: K-Mer Analysis
... Maybe the these pages can help you a bit further: Maximizing Utility of Available RAMs in K-mer World An Explanation of Velvet Parameter exp_cov ...
written 7.4 years ago by lgbi150
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Comment: C: Which New Bioinformatics Related Tool Would You Appreciate The Most?
... You could include taxonomic information based on the NCBI taxonomic databases to get species, genus, family, ... Visualisation of for example genus frequencies is often used in publications. ...
written 7.4 years ago by lgbi150
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Comment: C: Which New Bioinformatics Related Tool Would You Appreciate The Most?
... ViroBlast is only for viral sequences. NCBI Web-Blast gives results on a separate page for each input sequence: if you have a few 100s of them, you'll have to click a lot. Too easy... maybe, but there are some challenges and six months is not a lot. Of course, you can do it in 2 weeks and throw i ...
written 7.4 years ago by lgbi150
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Answer: A: Which New Bioinformatics Related Tool Would You Appreciate The Most?
... We often need to blast hundreds of 16S sequences and write per sequence the top < x > results in a table. This way we have a quick overview of what species our bacterial community may consist of. I personally do it with Biopython scripts or using standalone BLAST+, but I'm sure my wet-lab co ...
written 7.4 years ago by lgbi150 • updated 7.4 years ago by Dr. Mabuse47k
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Comparative Microbial Genomics
... Hi all, Our lab has sequenced 20 different strains of the same bacterial species. I now want to analyse these data, i.e., link genomic data to virulence (some of the strains are virulent, others aren't) and other phenotype differences. I started with de novo assemblies and mapping to an annotated ...
genomics comparative written 7.4 years ago by lgbi150 • updated 10 months ago by Biostar ♦♦ 20

Latest awards to lgbi

Student 6.3 years ago, asked a question with at least 3 up-votes. For 454 Sequences: Lower Case Base Call In Reverse Primer
Appreciated 7.4 years ago, created a post with more than 5 votes. For Comparative Microbial Genomics
Good Question 7.4 years ago, asked a question that was upvoted at least 5 times. For Comparative Microbial Genomics
Student 7.4 years ago, asked a question with at least 3 up-votes. For Comparative Microbial Genomics

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