influenza

[gsgs]

anyone interested to exchange data and/or utilities to analyze/organize
influenza-sequence databases ?

[Joann]

suggest collaboration

Perhaps this sequence collection may be interesting and useful joined in collaborative effort such as the Pandemic Influenza Digital Archive as described here.

researchfestival.nih.gov/sessiondetail.php?IC_ID=2656

[gsgs]

I had had no idea that such a thing existed.
Why was it kept secret ?
Aren't scientists being appropriately "rewarded" for publishing
their stuff ?

Alas, for this pandemic it comes too late.
Good however that it turned out to be "mild".
Maybe Moren's decision to publish was made at a time
when it looked worse...

[Joann]

see also

High Throughput Full Genome Sequencing of 2009 Swine H1N1 Isolates From World Wide Origins

Huo-Shu Houng, Ph.D., Viral Disease, Walter Reed Army Institute of Research
Novel 2009 inluenza A (H1N1) is a new flu virus of swine origin that was first detected in Mexico and the United States in March/April 2009. We systematically investigate the potential of ultra-deep pyrosequencing to determine and assemble full genome sequences of H1N1 viruses from world-wide geographic origins. A robust RT-PCR protocol was established to efficiently amplify across the boards of all 8 2009 novel H1N1 RNAs into sufficient cDNA quantities using the Roche 454 FLX system.

at http://www.healthtech.com/Conference....aspx?id=91502

and

Title: High-throughput Sequencing Pipeline for Complete Influenza A Viral Genomes from Clinical Samples: Nucleotide Polymporphisms, Antiviral Resistance, Ultra-Depth Sequencing Coverage and Clinical Relevance

Dr. Huo-Shu Houng, Division of Viral Diseases, Walter Reed Army Institute of Research, USA

at http://chinapharm.blog.163.com/blog/...0942382139816/

[gsgs]

are the sequences available ?

I have what is at genbank, but it's tedious to format,align,correct,sort etc.

it would be useful to share such improved databases

and provide upates

[gsgs]

as it happens the Walter Reed people had to resequence all their
influenza sequences. Apparently it's not so easy with high-throughput,
to assign the fragments to the correct viruses

[Joann]

Thank you for the update. Do you have any online references to updated material? Can you provide us with any further description on the progress of database curation on this topic and how such databases might be accessed?

[gsgs]

I assume they will submit updated sequences
but it can take a while

watch here for daily flu-updates:
ftp://ftp.ncbi.nih.gov/genomes/INFLUENZA/updates/

[Joann]

See also

See also Infuenza Research Database for detailed sequences information

http://www.fludb.org/brc/home.do?decorator=influenza