User: Csaba Kerepesi

gravatar for Csaba Kerepesi
Reputation:
320
Status:
Trusted
Location:
Hungary
Website:
http://kerepesi.web.el...
Twitter:
CsabaKerepesi
Scholar ID:
Google Scholar Page
Last seen:
10 months ago
Joined:
4 years ago
Email:
k*********@gmail.com

I am a student of the PhD School of Computer Science, Eötvös Loránd University, Hungary.My research interest is bioinformatics, particularly mathematical immunology and metagenomics analysis.

I have developed the metagenomic analysis tool AmphoraNet which is the webserver implementation of AMPHORA2 and AmphoraVizu which can visualize outputs generated by AMPHORA2 and AmphoraNet.

I am the creator of the Budapest Reference Connectome and the Giant Virus Finder.

Posts by Csaba Kerepesi

<prev • 19 results • page 1 of 2 • next >
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Tool: Giant Virus Finder - discover giant virus sequences in metagenomes
... I have developed a pipeline tool to find giant virus sequences in metagenomes. It called Giant Virus Finder and are available from the site of our group: Giant Virus Finder. This is the only tool specialized to find giant viruses. Using it we have found giant viruses sequences in metagenomes sample ...
tools written 23 months ago by Csaba Kerepesi320
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Answer: A: Getting species name after doing blastx?
... You can use MEGAN5 to process the blastx result file: http://ab.inf.uni-tuebingen.de/software/megan5/ It can work from gi numbers and displays taxids and scientific names. Alternatively if you want to write some scripts here are the mapping files: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ (check the ...
written 2.5 years ago by Csaba Kerepesi320
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Comment: C: Budapest Reference Connectome: a 3D visualization tool to browse connections in
... Thank you! Here is a new article of our research group (without me) about the differences of the connections between women's brains and men's brains: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130045 ...
written 2.5 years ago by Csaba Kerepesi320
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Tool: Budapest Reference Connectome: a 3D visualization tool to browse connections in the human brain
... I am pleased to announce a new tool in neuroscience (connectomics): Budapest Reference Connectome a 3D visualization tool to browse connections in the human (consensus) brain. The connectome has 1015 nodes, but those corresponding to the same larger cerebral area are drawn at the same spot, for a c ...
connectome neuroscience tool brain written 2.7 years ago by Csaba Kerepesi320 • updated 2.7 years ago by Mary11k
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Answer: A: pairwise comparison local BLAST
... Use the -subject option. But it will be faster if you generate database for each sequences. Furthermore I recommend use as low word size (-word_size) as you can. Default word size of blastn (megablast) is 28 which may be too high for your purpose. ...
written 2.8 years ago by Csaba Kerepesi320
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Comment: C: Why does the BLAST use E-value instead of p-value?
... Exactly: BLAST P-value: "The probability of a chance alignment occurring with a particular score or a better score in a database search." Quoted form BLAST Glossary More exactly: If you have an n length query sequence and an m length database and running BLAST you get a hit with S score, than the ...
written 2.8 years ago by Csaba Kerepesi320
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Answer: A: Why does the BLAST use E-value instead of p-value?
... Quote from the BLAST help (http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html#head4 ): "The BLAST programs report E-value rather than P-values because it is easier to understand the difference between, for example, E-value of 5 and 10 than P-values of 0.993 and 0.99995. However, when E < ...
written 2.8 years ago by Csaba Kerepesi320
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Answer: A: AmphoraNet, AmphoraVizu - fast metagenomic analysis online tools using phylogene
... Some important notes for users of AmphoraNet and AmphoraVizu: Citations show AmphoraNet are applied more times for genomic analyses Nature communications, Genome Announc. than for metagenomic analyses. Unfortunately I did not highlight this application possibility on the websites of the web serve ...
written 2.8 years ago by Csaba Kerepesi320
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Answer: A: randomly sequence cleavage - average length constraint
... One perl solution if there is no overlap: $Ln=1000; for ($i=int(rand(50))+1;$i<=$Ln;$i=$i+50) { printf "%d\n",$i+1-int(rand(3)); }     ...
written 2.8 years ago by Csaba Kerepesi320
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Comment: C: AmphoraNet, AmphoraVizu - fast metagenomic analysis online tools using phylogene
... I changed the sample pictures. ...
written 3.1 years ago by Csaba Kerepesi320

Latest awards to Csaba Kerepesi

Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Why does the BLAST use E-value instead of p-value?
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Why does the BLAST use E-value instead of p-value?
Scholar 2.8 years ago, created an answer that has been accepted. For A: Why does the BLAST use E-value instead of p-value?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Tools For Metagenomic Data Analysis
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.

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