gcg2 11% fetch sw:capb_chick Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. capb_chick.sw gcg2 12% fetch sw:capb_mouse Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. capb_mouse.sw gcg2 13% fetch sw:capb_human Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. capb_human.sw gcg2 14% fetch capb_caeel Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. capb_caeel.swissprot gcg2 15% gcg2 15% gcg2 15% gcg2 15% gcg2 15% pileup capb_*.* PileUp creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. 1 capb_caeel.swissprot 270 aa 2 capb_chick.sw 277 aa 3 capb_human.sw 272 aa 4 capb_mouse.sw 277 aa What is the gap creation penalty (* 8 *) ? What is the gap extension penalty (* 2 *) ? This program can display the clustering relationships graphically. Do you want to: A) Plot to a FIGURE file called "pileup.figure" B) Plot graphics on HP7550 attached to /dev/tty15 C) Suppress the plot Please choose one (* A *): The minimum density for a one-page plot is 4.0 sequences/100 platen units. What density do you want (* 4.0 *) ? What should I call the output file name (* pileup.msf *) ? fetch.msf Determining pairwise similarity scores... 1 x 2 3.63 1 x 3 3.63 1 x 4 3.62 2 x 3 4.79 2 x 4 5.14 3 x 4 4.82 Aligning... 1 .............-.. 2 .............-. .............-.. 3 .............-. .............-.. FIGURE instructions are now being written into pileup.figure. Total sequences: 4 Alignment length: 278 CPU time: 00.31 Output file:/disk2/usr/people/petang/LECTURE5/fetch.msf gcg2 16% cat fetch.msf !!AA_MULTIPLE_ALIGNMENT 1.0 PileUp of: capb_*.* Symbol comparison table: GenRunData:blosum62.cmp CompCheck: 6430 GapWeight: 8 GapLengthWeight: 2 fetch.msf MSF: 278 Type: P March 24, 2000 01:23 Check: 4767 .. Name: capb_chick Len: 278 Check: 3499 Weight: 1.00 Name: capb_mouse Len: 278 Check: 2774 Weight: 1.00 Name: capb_human Len: 278 Check: 1765 Weight: 1.00 Name: capb_caeel Len: 278 Check: 6729 Weight: 1.00 // 1 50 capb_chick MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA capb_mouse MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA capb_human MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA capb_caeel MGEQQLDCAL DLMRRLPPQH CDKNLTDLID LCPHLVDDLL STIDQPLKIA 51 100 capb_chick RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA capb_mouse RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA capb_human RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA capb_caeel ADRETGKQYL LCDYNRDGDS YRSPWSNTYD PPLEDGQLPS EKRRKMEIEA 101 150 capb_chick NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD capb_mouse NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD capb_human NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD capb_caeel NAAFESYRDL YFEGGVSSVY FWDLDNGGFA GIVLIKKEGD GAKNITGCWD 151 200 capb_chick SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKTGSGTMNL GGSLTRQMEK capb_mouse SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK capb_human SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK capb_caeel SIHVIEITER A..RQAHYKL TSTIMLWLQT NKSSSGVMNL GGSLTRQHEM 201 250 capb_chick DETVSDSSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSIDAI capb_mouse DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSLDAI capb_human DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSVQTF capb_caeel DAPINDQNTH LANMGRMIED QESKMRLTIN EIYFGKTKKV MSDLRSTEKQ 251 278 capb_chick PDNQKYKQLQ RELSQVLTQR QIYIQPDN capb_mouse PDNHKFKQLQ RELSQVLTQR QVYIQPDN capb_human ADKSKQEALK NDLVEALKRK QQC~~~~~ capb_caeel SELEKQDEIV RELNNAMANR GN~~~~~~