European Molecular
Biology Computing Network - Biocomputing Tutorials

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Hint List Index

Unix Basics
Exercise 1
Exercise 1 discussion

Sequence Fragement Assembly 1

Sequence Fragment Assembly 2

Sequence Editing and Exchange
Exercise 1

Sequence Databases

Typical (E)GCG Programmes
Exercise 3 discussion

Sequence Comparison
Exercise 1
Exercise 1

Searching Databases 1
Exercise 1

Multiple Sequence Analysis

Searching Databases 2

Other Programmes

Unix Basics

Exercise 1: Use redirection!

prompt> cat easyunix.txt > opinion.txt

Exercise 1 discussion: Use the append feature!

prompt> cat >> unixcmds.txt Type what you want to add. Use the return key <RETURN> to get to the next line(s). <RETURN> Use control-D to stop. <RETURN> <CTRL> D

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Sequence Fragement Assembly 1

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Sequence Fragment Assembly 2

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Sequence Editing and Exchange

Exercise 1: Use the UNIX pipe.

prompt> fromstaden contig.seq -out=contigcg.seq | topir contigcg.seq -out=contigcg.pir

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Sequence Databases

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Typical (E)GCC Programmes

Exercise 3 discussion: Info on ORFs, TATA boxes, etc., is in the Features Table of the original sequence entry. To sub-clone most of the coding sequence, you could perform a double digest with AluI & BmgI. Or you could look for enzymes that cut outside the ORF using the "-excl=" switch. Try the command below. You could also use mapplot, but remove the "-out=" switch if you do!

prompt> map hsfau.ge_pr -out=hsfau4.map -minc=1 -maxc=3 -excl=50,465

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Sequence Comparison

Exercise 1: Exclude the best region to find the second best region. This means doing two more bestfit runs, one on each "side" of the best region, and comparing the quality scores for the two alignments found.

prompt> bestfit pdrhod.ge_in rnops.ge_ro begin1=1 begin2=1 end1=982 end2=961 -out=rhodop2a.pair prompt> bestfit pdrhod.ge_in rnops.ge_ro begin1=1022 begin2=1001 end1=1675 end2=1493 -out=rhodop2b.pair prompt> more rhodop2a.pair ... prompt> more rhodop2b.pair ...

Exercise 1: Ask for vertical bars with base similarities.

prompt> gapshow -che ... prompt> gapshow pdrhod.ge_in rnops.ge_ro -begin1=982 begin2=961 end1=1022 end2=1001 -bars=s

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Searching Databases 1

Exercise 1: Map them for EcoRI sites.

prompt> map @gofishmrnaecor1.list -enz=ecor1 -out=gofishclone.map -minc=2 prompt> more gofishclone.map

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Multiple Sequence Analysis

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Searching Databases 2

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Other Programmes

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Comments? Questions? Accolades?
Please send them to David Featherston ( dwf@biobase.dk )