ANSWER EX90-05 IRIX (gcg2) login: petang Password: Copyright 1987-1997 Silicon Graphics, Inc. All Rights Reserved. Last login: Sat Mar 23 22:11:22 CST 2002 by UNKNOWN@210.208.177.62 You have mail. ********************************************************************** * WELCOME TO THE NHRI GCG SERVER ! * * * * * * Type go to start the GCG Package ! * * === * * * * Type gcgm to start the manual driven GCG Package ! * * === * * * * Online help: % genhelp or http://gcg.nhri.org.tw * * * * problem report by email: gcg@nhri.org.tw * * * ********************************************************************** gcg2 1% go gcg2 2% gcg2 2% mkdir LECTURE5 gcg2 3% ls CASPASE CeLR LECTURE5 RACE TVCDC WEIMIN CP DAT PRACTICE SEQUENCING TVLDLR gcg2 4% cd LECTURE5 gcg2 5% fetch genbank:k02938 Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. k02938.gb_ov gcg2 6% fetch genbank:x15785 Fetch copies GCG sequences or data files from the GCG database into your directory or displays them on your terminal screen. x15785.gb_ov gcg2 7% bestfit BestFit makes an optimal alignment of the best segment of similarity between two sequences. Optimal alignments are found by inserting gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman. BESTFIT of what sequence 1 ? k02938.gb_ov Begin (* 1 *) ? End (* 1518 *) ? Reverse (* No *) ? to what sequence 2 (* k02938.gb_ov *) ? x15785.gb_ov Begin (* 1 *) ? End (* 515 *) ? Reverse (* No *) ? What is the gap creation penalty (* 50 *) ? What is the gap extension penalty (* 3 *) ? What should I call the paired output display file (* k02938.pair *) ? best.pai r Aligning .........................-. Aligning .........................-. Gaps: 0 Quality: 654 Quality Ratio: 8.959 % Similarity: 94.521 Length: 73 gcg2 8% cat best.pair BESTFIT of: k02938.gb_ov check: 6524 from: 1 to: 1518 LOCUS XELTFIIIA 1518 bp mRNA VRT 28-APR-1993 DEFINITION X.laevis 5S RNA gene transcription factor (TFIIIA) mRNA, complete cds. ACCESSION K02938 VERSION K02938.1 GI:214818 KEYWORDS developmental regulation; transcription factor. . . . to: x15785.gb_ov check: 238 from: 1 to: 515 LOCUS XLTF3A5 515 bp DNA VRT 03-DEC-1998 DEFINITION Xenopus laevis TFIIIA gene 5' region and partial coding region. ACCESSION X15785 VERSION X15785.1 GI:65120 KEYWORDS developmental regulation; TFIIIA gene; transcription factor; transcription factor IIIA; zinc finger protein. . . . Symbol comparison table: /usr/people/gcg/gcgcore/data/rundata/swgapdna.cmp CompCheck: 2335 Gap Weight: 50 Average Match: 10.000 Length Weight: 3 Average Mismatch: -9.000 Quality: 654 Length: 73 Ratio: 8.959 Gaps: 0 Percent Similarity: 94.521 Percent Identity: 94.521 Match display thresholds for the alignment(s): | = IDENTITY : = 5 . = 1 k02938.gb_ov x x15785.gb_ov March 24, 2000 01:14 .. . . . . . 8 GGAAGCCGAGGGCTGTTCAGTTGCTGAAGGAGAGATGGGAGAGAAGGCGC 57 ||||||||||||| | | |||| ||||||||||||||||||||||||||| 443 GGAAGCCGAGGGCAGCTTAGTTACTGAAGGAGAGATGGGAGAGAAGGCGC 492 . . 58 TGCCGGTGGTGTATAAGCGGTAC 80 ||||||||||||||||||||||| 493 TGCCGGTGGTGTATAAGCGGTAC 515 gcg2 9% gap Gap uses the algorithm of Needleman and Wunsch to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP of what sequence 1 ? k02938.gb_ov Begin (* 1 *) ? End (* 1518 *) ? Reverse (* No *) ? to what sequence 2 (* k02938.gb_ov *) ? x15785.gb_ov Begin (* 1 *) ? End (* 515 *) ? Reverse (* No *) ? What is the gap creation penalty (* 50 *) ? What is the gap extension penalty (* 3 *) ? What should I call the paired output display file (* k02938.pair *) ? gap.pair Aligning .........................-. Aligning .........................-... Gaps: 2 Quality: 1789 Quality Ratio: 3.474 % Similarity: 37.160 Length: 1519 gcg2 10% cat gap.pair GAP of: k02938.gb_ov check: 6524 from: 1 to: 1518 LOCUS XELTFIIIA 1518 bp mRNA VRT 28-APR-1993 DEFINITION X.laevis 5S RNA gene transcription factor (TFIIIA) mRNA, complete cds. ACCESSION K02938 VERSION K02938.1 GI:214818 KEYWORDS developmental regulation; transcription factor. . . . to: x15785.gb_ov check: 238 from: 1 to: 515 LOCUS XLTF3A5 515 bp DNA VRT 03-DEC-1998 DEFINITION Xenopus laevis TFIIIA gene 5' region and partial coding region. ACCESSION X15785 VERSION X15785.1 GI:65120 KEYWORDS developmental regulation; TFIIIA gene; transcription factor; transcription factor IIIA; zinc finger protein. . . . Symbol comparison table: /usr/people/gcg/gcgcore/data/rundata/nwsgapdna.cmp CompCheck: 8760 Gap Weight: 50 Average Match: 10.000 Length Weight: 3 Average Mismatch: 0.000 Quality: 1789 Length: 1519 Ratio: 3.474 Gaps: 2 Percent Similarity: 37.160 Percent Identity: 37.160 Match display thresholds for the alignment(s): | = IDENTITY : = 5 . = 1 k02938.gb_ov x x15785.gb_ov March 24, 2000 01:16 .. . . . . . . . . 301 AGGCAAACATGAAGAAGCACTTTAACAGATTCCATAACATCAAGATCTGC 350 | || | | | | | || | | | 1 ..............AGATCTATTGAGAAAGGGCCTTACTGTGTGCTGTAA 36 . . . . . 351 GTCTATG.TGTGCCATTTTGAGAACTGTGGCAAAGCATTCAAGAAACACA 399 | ||| ||| | | | | | | |||| | | 37 TTAGATGCTGTTAGTTATCGCACTCCTGTGTGGACCATTGCATCCATCAC 86 . . . . . 400 ATCAATTAAAGGTTCATCAGTTCAGTCACACACAGCAGCTGCCATACGAA 449 || | | || | || || ||| |||| ||||| || 87 ATTCACAACAGTTACAGTTTCTCCAACACCAGCAGCTGCTGCACACCGTT 136 . . . . . 450 TGTCCTCATGAAGGCTGTGACAAGCGGTTTTCTTTGCCTTCCCGTTTAAA 499 | | | | | | || | | | || | || | ||| 137 TCCTCGGCTTCATGTATTATCACGTGCTCCACTAGGACTCAACCACTAAG 186 . . . . . 500 ACGTCATGAAAAAGTCCATGCAGGCTATCCCTGCAAAAAGGATGATTCTT 549 | | | | | | | ||| | | || 187 AACGAGGGGAGTGTCCAGAAACACCCAACTTGTGAAATAACACATCGCTG 236 . . . . . 550 GCTCATTTGTGGGAAAGACTTGGACATTATACTTGAAACACGTGGCAGAA 599 | | | || | || | || | || || 237 ACATAAAACACAGGAATTTAACATCCTTTTTTTTAAGTTTGCGAGCGCAA 286 . . . . . 600 TGCCATCAGGACCTAGCAGTATGTGATGTGTGTAATCGAAAATTCAGGCA 649 | | ||| ||| | | | || | || | ||| 287 TTACTGAAGGCTAAAGCTGCAAGGGACACAGGAAAGGGCTGATTGCCAAT 336 . . . . . 650 CAAAGATTACTTGAGGGATCATCAGAAAACTCACGAAAAAGAGCGAACTG 699 | || | | | || | | | | | | || | 337 CCTTTCAGACATCGCAAAACTTC......CCGATGCATGTGCGATAATGG 380 . . . . . 700 TGTATCTCTGCCCTCGAGATGGCTGTGACCGCTCCTATACCACTGCATTC 749 | | || | || | | | | | || || ||| 381 TTTGTCCTAGAGCTATATAAACAGGCACACATGGCGGCTACAGTGGCTTC 430 . . . . . 750 AATCTTAGAAGCCATATACAATCATTTCATGAGGAACAGAGACCTTTTGT 799 | || | | | | | | || || 431 TACAAGTTCAGAGGAAGCCGAGGGCAGCTTAGTTACTGAAGGAGAGATGG 480 . . . . . 800 TTGTGAGCATGCTGGCTGCGGGAAATGCTTTGCAATGAAAAAAAGCCTAG 849 | || |||| | | || || | | 481 GAGAGAAGGCGCTGCCGGTGGTGTATAAGCGGTAC............... 515 . . . 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~~~~~~ gcg2 17% ls best.pair capb_human.sw k02938.gb_ov capb.txt capb_mouse.sw pileup.figure capb_caeel.swissprot fetch.msf x15785.gb_ov capb_chick.sw gap.pair gcg2 18% pileup @capb.txt 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_CHICK 277 aa 2 CAPB_MOUSE 277 aa 3 CAPB_HUMAN 272 aa 4 CAPB_CAEEL 270 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 (* capb.msf *) ? list.msf Determining pairwise similarity scores... 1 x 2 5.14 1 x 3 4.79 1 x 4 3.63 2 x 3 4.82 2 x 4 3.62 3 x 4 3.63 Aligning... 1 .............-.. 2 .............-. .............-.. 3 .............-. .............-.. FIGURE instructions are now being written into pileup.figure. Total sequences: 4 Alignment length: 278 CPU time: 00.34 Output file:/disk2/usr/people/petang/LECTURE5/list.msf gcg2 21% pretty fetch.msf{*} Pretty displays multiple sequence alignments and calculates a consensus sequence. It does not create the alignment; it simply displays it. fetch.msf{capb_chick} len: 278 wgt: 1.00 fetch.msf{capb_mouse} len: 278 wgt: 1.00 fetch.msf{capb_human} len: 278 wgt: 1.00 fetch.msf{capb_caeel} len: 278 wgt: 1.00 Begin (* 1 *) ? End (* 278 *) ? What should I call the output file (* pretty.pretty *) ? fetch.pretty gcg2 22% cat fetch.pretty PRETTY of: fetch.msf{*} March 24, 2000 01:31 .. 1 50 fetch.msf{capb_chick} MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA fetch.msf{capb_mouse} MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA fetch.msf{capb_human} MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA fetch.msf{capb_caeel} MGEQQLDCAL DLMRRLPPQH CDKNLTDLID LCPHLVDDLL STIDQPLKIA 51 100 fetch.msf{capb_chick} RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA fetch.msf{capb_mouse} RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA fetch.msf{capb_human} RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMPS ARLRKLEVEA fetch.msf{capb_caeel} ADRETGKQYL LCDYNRDGDS YRSPWSNTYD PPLEDGQLPS EKRRKMEIEA 101 150 fetch.msf{capb_chick} NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD fetch.msf{capb_mouse} NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD fetch.msf{capb_human} NNAFDQYRDL YFEGGVSSVY LWDLDH.GFA GVILIKKAGD GSKKIKGCWD fetch.msf{capb_caeel} NAAFESYRDL YFEGGVSSVY FWDLDNGGFA GIVLIKKEGD GAKNITGCWD 151 200 fetch.msf{capb_chick} SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKTGSGTMNL GGSLTRQMEK fetch.msf{capb_mouse} SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK fetch.msf{capb_human} SIHVVEVQEK SSGRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK fetch.msf{capb_caeel} SIHVIEITER A..RQAHYKL TSTIMLWLQT NKSSSGVMNL GGSLTRQHEM 201 250 fetch.msf{capb_chick} DETVSDSSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSIDAI fetch.msf{capb_mouse} DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSLDAI fetch.msf{capb_human} DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VNGLRSVQTF fetch.msf{capb_caeel} DAPINDQNTH LANMGRMIED QESKMRLTIN EIYFGKTKKV MSDLRSTEKQ 251 278 fetch.msf{capb_chick} PDNQKYKQLQ RELSQVLTQR QIYIQPDN fetch.msf{capb_mouse} PDNHKFKQLQ RELSQVLTQR QVYIQPDN fetch.msf{capb_human} ADKSKQEALK NDLVEALKRK QQC~~~~~ fetch.msf{capb_caeel} SELEKQDEIV RELNNAMANR GN~~~~~~ gcg2 23% prettybox fetch.pretty PrettyBox displays multiple sequence alignments in PostScript format, using shading to represent regions that agree with a calculated consensus sequence. The program does not create the alignment; it simply displays it. PRETTYBOX what sequences ? fetch.msf{*} fetch.msf{capb_chick}, len: 278 fetch.msf{capb_mouse}, len: 278 fetch.msf{capb_human}, len: 278 fetch.msf{capb_caeel}, len: 278 Begin (* 1 *) ? End (* 278 *) ? Print in which orientation: l)andscape p)ortrait Please select (* L *): Display a consensus (* No *) ? y Find consensus to what minimum plurality (* 2.00 *) ? Where should numbers be placed: r)ight side t)op n)one Please select (* R *): What should I call the output PostScript file (* prettybox.ps *) ? fetch.ps gcg2 25% ls best.pair capb_mouse.sw k02938.gb_ov capb.txt fetch.msf list.msf capb_caeel.swissprot fetch.pretty pileup.figure capb_chick.sw fetch.ps pretty.pretty capb_human.sw gap.pair x15785.gb_ov gcg2 26%