MBG 8680: Computer Applications in Molecular Genetics

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ADVANCED GCG FUNCTIONS


START SEQLAB

start the X Windows program on your PC
telnet to genetics, set DISPLAY: setenv DISPLAY ip.address:0
cd into your mbg8680/gcg folder: cd mbg8680/gcg
type gcg, then type seqlab &
Make sure your working dir is set to mbg8680/gcg
Make sure your working list is set to mbg8680.list
(see Introduction to GCG for a review if needed)

ADD NEW PROTEIN SEQUENCE TO LIST

Click File, Add Sequences From, Sequence Files
Under Filter, change it to *.pep, then click Filter
Click hs7c_human.pep, click Add, click Close
Click File, click Save List

ADVANCED PROTEIN SEQUENCE ANALYSES

This searches for sequence motifs in the amino acid sequence.

Click the hs7c_human.pep sequence to select it.
Click Functions, Protein Analysis, Motifs
Click Run (note options available).
Click Windows, Job Manager, Open Output Mgr
Dislplay the Motifs results file, examine the motifs found.
Close Display, then close Output and Job Manager Windows.

This searches for structural motifs in a protein.

Click Functions, Protein Analysis, Profile Scan, Run
Click Windows, Job Manager, Open Output Mgr
Click Display, examine the matches found.
Close Display, then close Output and Job Manager Windows.

These programs examine different aspects of protein structure.

Run Isoelectric, Pepplot, and Peptidestructure
Note 2 output files from Peptidestructure
Display the .figure file, then zoom in on part of the structure.

Run PlotStructure on the .p2s datafile, and run it for antegenicity.

Run Helicalwheel on the 1st 14 amino acids only.

PATTERNS IN NUCLEIC ACID SEQUENCES

This searches for transcription factor binding sites in a DNA sequence.

Run Findpatterns on the mbg8680.seq file
For Search Set, Add Main List Selection, select mbg8680.seq, Add, Close
For Patterns, type genmoredata:tfsites.dat, Add All, Close, Run

To learn more about the sites, use the GCG fetch program to bring back
a copy of the tfsites.dat file and examine the list of sites in the file.

DATABASE SEARCHING

This searches for similarity of a given sequence to all the sequences in 
a database.

Select the mbg8680.seq entry from the mbg8680.list file.
Click Functions, Database Sequence Searching, NetBlast.
Note options, then click Run.
Click Windows, Job Manager, Open Output Mgr
Display the .netblast file and examine the results.

NB: NetBlast searches the databases at NCBI, whereas Blast and FastA 
search the databases on the genetics computer (NetBlast is MUCH faster on
the high speed mainframes at NCBI, IF their servers are up!).

NetFetch can be used to retrieve sequence files from NCBI, such as 
sequences listed in a NetBlast results file.
Send comments to: dwomble@genetics.wayne.edu
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