User: gislevestergaard

Reputation:
10
Status:
New User
Location:
Germany
Website:
http://www.helmholtz-m...
Scholar ID:
Google Scholar Page
Last seen:
4 years, 11 months ago
Joined:
5 years, 9 months ago
Email:
g***************@gmail.com

Gisle Vestergaard joined the group of Michael Schloter in 2014 as a postdoctoral fellow funded by the European project Phyto2Energy. His main focus is on the use of gene synteny for both functional annotation and detection of recent gene mobilization, which will be utilized in the Phyto2Energy project to investigate heavy metal resistance genes.
He got his Masters in biochemistry at the University in Copenhagen (2003-2006) and received a PhD scholarship from the University of Copenhagen (2006-2009), which he did under the supervision of Prof. Roger A. Garrett. During this time he was involved in the characterization of several novel virus families using molecular biology tools and bioinformatical analysis of the viral genomes. During his first postdoctoral position at the Danish Archaea Centre (2009-2011) he did bioinformatical analysis of CRISPR/Cas-systems, the immune-system found in both archaea and bacteria. During his second postdoc at the Molecular Microbial Ecology Group of Prof. Søren J. Sørensen (2011-2014), he worked on determining significant recipient factors with regards to their ability of plasmid uptake and developed pipelines to investigate gene synteny in both public databases and metagenomes.
Selected works:
Haring M, Vestergaard G, Rachel R, Chen L, Garrett RA, et al. (2005) Virology: independent virus development outside a host. Nature 436: 1101–1102.
Vestergaard G, Aramayo R, Basta T, Haring M, Peng X, et al. (2008) Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses. Journal of Virology 82: 371–381.
Vestergaard G, Garrett RA, Shah SA (2014) CRISPR adaptive immune systems of Archaea. RNA Biology 11: 156–167.

Posts by gislevestergaard

<prev • 4 results • page 1 of 1 • next >
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Comment: C: Blastall gives several hits to the same subject sequence
... Will talk to sysadm and report back, thanks again! ...
written 5.1 years ago by gislevestergaard10
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Comment: C: Blastall gives several hits to the same subject sequence
... First of all, thanks for taking the time...the blast is obviously strong with you :-) Using Package: blast 2.2.27, build Mar 23 2013 16:48:04 I tried blastp -db ~/genomics/NCBI/Refseq/Prot/complete.nonredundant_protein.faa -out test.blastplus -max_target_seqs 20 -max_hsps 1 -outfmt 6 -query test. ...
written 5.1 years ago by gislevestergaard10
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Answer: A: Blastall gives several hits to the same subject sequence
... The only solution I have found is to subsequently use sort on the output file. Since the list is already sorted by query, subject and then e-val, you are able to do: cat test.output | sort -u -k1,2 Update: If able, use blast+ version => 2.2.29 and see accepted answer else  this still seems to ...
written 5.1 years ago by gislevestergaard10
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Blastall gives several hits to the same subject sequence
... Short query sequences will sometimes give several hits to the same (often large) subject sequence. This is problematic if you ask for the 20 best hits since blastall will actually give you the best hits to 20 subject sequences. Thus using the following query: IVLFGGSAVNGLLADTWQFDGTRWQQVAAVVANTAPNTAP ...
blast written 5.1 years ago by gislevestergaard10 • updated 5.1 years ago by hpmcwill1.1k

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