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location Athens, Greece
age 34
visits member for 2 years, 7 months
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Elected moderator on Unix & Linux. Feel free to @ping me in chat if there's anything I can help you with.

I am a computational biologist with a background in biology, not computers. My PhD work was on gene prediction and comparative genomics but my current research is in systems biology, specifically protein-protein interaction networks.

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May
7
revised What does chromosome CHR_Un, CHR_MT in the ftp site of NCBI mean?
Made the formatting homogeneous.
May
6
comment translation of scientific names
This question appears to be off-topic because it is about nomenclature and the meanings of words in dead languages, not biology.
May
6
comment translation of scientific names
All you need to do is use a Latin/English and/or Greek/English dictionary. This is not really related to biology but linguistics.
May
5
comment Genome Project Focusing on gene ADRB2?
I ask again, please clarify. Arg/Arg16 is not a gene, its a genotype; I think the gene you mean is ADRB2. You still have not told us what is missing from the tools you are using. You have not explained what exactly you want to visualize nor what exactly you are looking at. I am beginning to guess you are after SNP variations but I'm not sure. You mention vertebrates, does that mean you want to do a comparative analysis of some sort? Please edit and be more specific.
May
4
comment Genome Project Focusing on gene ADRB2?
@Masi, all of them do that, that's the point og a genome browser. Can you please edit your question and narrow it down? I still don't know what you need that neither the UCSC nor Ensembl offer you. The only way to choose between them is personal choice or specific tools provided but since you don't explain what you want to do, it's hard to help.
May
4
comment Genome Project Focusing on gene ADRB2?
I don't understand what you're asking. Ensembl has subsections that let you look at a single genomes. The fact that the database has other genomes is irrelevant. What are you calling the "original Human Genome Project"? Do you mean UCSC? What kind of data do you want to visualize?
May
4
revised Genome Project Focusing on gene ADRB2?
added 2 characters in body
May
4
comment Whole genome amino acid composition tool?
@Masi could you clarify how you would like the answer to be improved? Perhaps edit the question to define a specific statistical calculation you would like to see?
Apr
28
comment Modern alternatives of DNA footprinting
@canadianer ah! DNAse footprinting, OK.
Apr
28
comment Modern alternatives of DNA footprinting
Identify it as what? Guess the species of origin? Guess the individual it came from? Guess its function?
Apr
28
comment PDB file for Osteopontin (SPP1)
Is the structure known?
Apr
26
comment Sequence alignment scoring
@daniel the -4 in your score is because a T in seq1 aligned to a - in seq2 has a score of -4 in the table. The -1 is because TT has a score of -1 in the table. However, while I have actually worked with this kind of thing, I have never worked with it in depth and it was a few years ago now, I may well be wrong.
Apr
26
comment Sequence alignment scoring
@daniel in which case it is probably mistaken (my approach, not your text). Taking what you show out of context, I am simply using the score for each position. So, since T- has a score of -10 in your table, I am using that.
Apr
26
answered Sequence alignment scoring
Apr
26
comment Sequence alignment scoring
Could you explain how you get that -17? A gap costs between -2 and -10 depending on which one in the table in the OP. The score of the mismatch also changes. Where are your numbers coming from?
Apr
26
revised Sequence alignment scoring
edited tags
Apr
26
comment chimeric sequences
Do you mean chimeric sequences that are artifacts of the sequencing process or actual bona fide chimeric transcripts that are present in vivo?
Apr
25
comment psychological database with sequenced DNA records
I would be very surprised if such a thing exists. Apart from the privacy issues (OK, you can anonymize the data), there aren't to my knowledge any projects for such large scale sequencing of human samples. The closest I can think of is the 1000 genomes project but I doubt any psychological data will be included.
Apr
23
comment How to determine whether the energy of a stem-loop fold is significant or not?
A predicted stem loop of what? A nucleotide chain presumably, and most likely RNA but you need to tell us.
Apr
21
comment is there a way to do batch download for all gene pathways?
What pathways? From which database? What species?