User: pevsner
pevsner • 420
- Reputation:
- 420
- Status:
- Trusted
- Location:
- Kennedy Krieger Institute (Baltimore, MD)
- Website:
- http://pevsnerlab.kenn...
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 4 years, 4 months ago
- Email:
- p******@kennedykrieger.org
My lab studies childhood brain diseases using tools of bioinformatics and genomics.
Posts by pevsner
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... Hello, here's some information about the origin of +5/-4.
Please see the section "BLASTN reward/penalty values" on the BLAST® Command Line Applications User Manual at https://www.ncbi.nlm.nih.gov/books/NBK279684/. That page offers Table D1 with the +5 for matches, -4 for mismatches scoring scheme a ...
written 4 months ago by
pevsner • 420
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... Here's a place to download PAM and BLOSUM matrices (and Dayhoff, GONNETT):
ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/
Jones matrices are here:
ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum/JTT/
RBLOSUM62 and RBLOSUM64 are given here as a PDF:
http://web.mit.edu/bamel/blosum/styczynski2007su ...
written 4 months ago by
pevsner • 420
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... Here are some concepts about evolution you can learn from your phylogenetic tree.
Given that your tree is constructed from sequences that are from different species, you can use your tree to ask which species last shared a common ancestor. In the case of mammals there is tremendous interest in k ...
written 3.3 years ago by
pevsner • 420
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... You can copy and paste these 9 accession numbers into NCBI Nucleotide and see that five are from the EST database. Of the four that are RefSeq accessions, two have been updated and two have had their records removed.
...
written 3.3 years ago by
pevsner • 420
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... To me it's easiest to understand the key biological issues underlying protein scoring matrices by taking a historical view. In the 1960s researchers solved the primary amino acid sequence of many hundreds of proteins and grouped them into families such as cytochromes c and globins. When you align tw ...
written 3.3 years ago by
pevsner • 420
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... Hi virus_n00b: great questions but no, your statements are not correct. Here are some suggestions on how to think about phylogenetic trees.
There are nodes that are either terminal (your data sequences v1 to v11) or internal (inferred ancestral sequences; some software packages allow you to see t ...
written 3.3 years ago by
pevsner • 420
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... Your query about monographs on tuberculosis is excellent because each species has its own unique story to tell. Tuberculosis claims more lives than any other infectious agent and it's compelling to study that genome (in terms of e.g. host responses, resistance to treatment, evolutionary history, spe ...
written 3.3 years ago by
pevsner • 420
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... Yes, you can use the FASTQ files you download using SRA Toolkit (or FASTQ files you get from any source) for a variety of purposes such as assembly or alignment to a reference genome. Many people consider it a good idea to assess the quality of the reads in your file, and FastQC is a very popular to ...
written 3.3 years ago by
pevsner • 420
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... Yes you're right, you do need to download a reference genome and you do generate a SAM file locally. But the advantage of using HISAT with NCBI-NGS toolkit is that you don't need to download reads in the FASTQ format and those are often large. So it's not quite downloading the whole thing and I beli ...
written 3.3 years ago by
pevsner • 420
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... Here's an example of how to analyze RNA-seq data from SRA (without using Galaxy and without downloading the data!). First you need four things.
Obtain an SRR accession of interest, i.e. a set of RNA-seq runs from the SRA database at NCBI. Try browsing the SRA website, then use the "Send to" pulld ...
written 3.3 years ago by
pevsner • 420
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