User: Emempe
Emempe • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Munich, Germany
- Last seen:
- 7 years, 6 months ago
- Joined:
- 10 years ago
- Email:
- m*************@googlemail.com
Posts by Emempe
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... I would like to extract all data for human (and later mouse) from TargetScan but I can't quite wrap my head around the different files offered by TargetScan and relationships between them: http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61
I would like to get the (from a biol ...
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... Thanks! I think I have to write an output function myself ... one would have to put it in blocks of 60, 80 or whatever nucleotides. ...
written 8.9 years ago by
Emempe • 30
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... I do a simple pairwise DNA sequence alignment with pairwiseAlignment from the Biostrings package in Bioconductor:
library('Biostrings')
seq1 = 'ATGCTA'
seq2 = 'ATGTA'
pairwiseAlignment(pattern = seq1, subject = seq2)
The output looks as follows:
Global PairwiseAlignedFixedSubject (1 of 1)
patter ...
written 8.9 years ago by
Emempe • 30
• updated
8.9 years ago by
Steve Lianoglou ♦ 5.1k
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... I use MATLAB with the Bioinformatics Toolbox to do pairwise sequence alignments:
[GlobalScore, GlobalAlignment] = nwalign(seq1,seq2);
Showalign is used to display the data:
showalign(GlobalAlignment)
But how can I write the data to a file that is formatted like 'showalign'?
Thanks and cheers
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... Thanks, that helps a lot! Do you know if BioMart is accessible via Bioconductor/Matlab Bioinformatics Toolbox to put this in a script? ...
written 9.5 years ago by
Emempe • 30
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... Thanks for your reply, but my question aims at finding genes within the rat genome (rather than associate more information with this genes). Once I have the genes, I will look into it. I think mapping to mouse/human could be interesting. ...
written 9.5 years ago by
Emempe • 30
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... I have a large list of genomic positions for the latest assembly of the rat genome (rn4). I would like to map those positions onto the genome and get a list of protein coding genes that lie in the same regions.
More specifically, my questions are:
I understand that the Rat Genome Sequencing Cons ...
written 9.5 years ago by
Emempe • 30
• updated
9.5 years ago by
Bert Overduin • 3.7k
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