User: Emempe

gravatar for Emempe
Emempe30
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

<prev • 7 results • page 1 of 1 • next >
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Which File Should I Use To Get All Predictions From Targetscan?
... 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 ...
prediction target written 7.6 years ago by Emempe30 • updated 5.0 years ago by Biostar ♦♦ 20
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Comment: C: R/Biostring: Print Sequence Alignment To File
... 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 Emempe30
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R/Biostring: Print Sequence Alignment To File
... 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 ...
sequence bioconductor alignment written 8.9 years ago by Emempe30 • updated 8.9 years ago by Steve Lianoglou5.1k
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Matlab: Write Pairwise Sequence Alignment To File
... 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 ...
sequence alignment matlab written 9.3 years ago by Emempe30 • updated 7.0 years ago by Biostar ♦♦ 20
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Comment: C: Map Genomic Positions Onto Rat Genome
... 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 Emempe30
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Comment: C: Map Genomic Positions Onto Rat Genome
... 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 Emempe30
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Map Genomic Positions Onto Rat Genome
... 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 ...
genome annotation mapping written 9.5 years ago by Emempe30 • updated 9.5 years ago by Bert Overduin3.7k

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