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grep, agrep, cut, sort and
wc are
very useful UNIX tools to
get a quick overview of text files or extract certain information
from files. Use these tools to answer the following questions:
- Browse to the EBI website
and download an EMBL formatted file
of all nucleotide sequences from Rat-kangaroos
(Potoroidae).
- How many sequences are available? Did the download
succeed? (Sometimes huge batch downloads break, so it is
always a good idea to check if all sequences were retrieved!)
- How many of the entries have the feature key 5'UTR?
- How many and which tRNA-genes are annotated?
- A very useful tool to convert files between different formats is readseq. Try the web version at http://www.ebi.ac.uk/cgi-bin/readseq.cgi to convert the formats and extract features.
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