Exercise05

(1)BestFit and GAP
"fetch" the following sequences:
genbank:k02938 (k02938.gb_ov) (Xenopus 5S RNA gene transcription factor TFIIIA mRNA)
genbank:x15785 (x15785.gb_ov) (Xenopus TFIIIA gene 5' region)

Perform 
(A)bestfit-name the output display file best.pair
(B)gap-name the output display file gap.pair
-->cat best.pair
-->cat gap.pair
-->Compare the results

(2)For PileUP
"fetch" the following sequences:
uniprot:capzb_chick
uniprot:capzb_mouse
uniprot:capzb_human
uniprot:capzb_caeel
-->Perform pileup capzb_*.*
-->call the output display file fetch.msf

(3)Create a list file in PC as follows
!!SEQUENCE_LIST 1.0
..
uniprot:capzb_chick
uniprot:capzb_mouse
uniprot:capzb_human
uniprot:capzb_caeel
-->and save as capzb.txt
-->use ftp to transfer the file to your GCG account
-->pileup @capzb.txt
-->call the output display file list.msf
-->Compare list.msf and fetch.msf

(4)Use "Pretty" to display *.msf files
-->pretty fetch.msf{*}
-->call the output display file fetch.pretty
-->cat fetch.pretty

(5)Use "Prettybox" to display pretty result
-->prettybox fetch.msf{*}
-->call the output display file fetch.ps
-->use FTP to transfer file to you PC
-->Use Photoshop, CorelDraw, Paintshop Pro or Ghostview to open the file
-->Download gsv27550.exe from ftp://163.25.92.42/softwares/ghostview.

(6)Use "GeneDoc" to Display msf.files
-->Download gsv27550.exe from ftp://163.25.92.42/softwares/ghostview.