Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

This commit was manufactured by cvs2svn to create tag

'bioperl-release-1-2-2'.

svn path=/bioperl-live/tags/bioperl-release-1-2-2/; revision=6621
  • Loading branch information...
commit f05e70852d02687d7e3dcb6da13862c133ec6a10 1 parent f07cf87
nobody authored
View
286 Bio/Expression/FeatureGroup.pm
@@ -1,286 +0,0 @@
-# $Id$
-# BioPerl module for Bio::Expression::FeatureGroup
-#
-# Copyright Allen Day <allenday@ucla.edu>, Stanley Nelson <snelson@ucla.edu>
-# Human Genetics, UCLA Medical School, University of California, Los Angeles
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA
-Bio::Expression::FeatureI
-
-=head1 SYNOPSIS
-
-#
-
-=head1 DESCRIPTION
-
-A set of DNA/RNA features.
-
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to one
-of the Bioperl mailing lists. Your participation is much appreciated.
-
- bioperl-l@bioperl.org - General discussion
- http://bioperl.org/MailList.shtml - About the mailing lists
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.
- Bug reports can be submitted via email or the web:
-
- bioperl-bugs@bio.perl.org
- http://bugzilla.bioperl.org/
-
-=head1 AUTHOR
-
-Allen Day E<lt>allenday@ucla.eduE<gt>
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object
-methods. Internal methods are usually preceded with a _
-
-=cut
-
-# Let the code begin...
-package Bio::Expression::FeatureGroup;
-
-use strict;
-
-use base qw(Bio::Root::Root Bio::Expression::FeatureI);
-use vars qw($DEBUG);
-
-=head2 new
-
- Title : new
- Usage : $featuregroup = Bio::Expression::FeatureGroup->new(%args);
- Function: create a new featuregroup object
- Returns : a Bio::Expression::FeatureGroup object
- Args : an optional hash of parameters to be used in initialization:
- -id -- the featuregroup ID
- -type -- the featuregroup type
-
-=cut
-
-sub new {
- my($class,@args) = @_;
- my $self = bless {}, $class;
- $self->_initialize(@args);
- return $self;
-}
-
-=head2 _initialize
-
- Title : _initialize
- Usage : $featuregroup->_initialize(@args);
- Function: initialize the featuregroup object
- Returns : nothing
- Args : @args
-
-=cut
-
-sub _initialize{
- my ($self,@args) = @_;
- my %param = @args;
-
- $self->type($param{-type});
- $self->id($param{-id} );
-
- $self->SUPER::_initialize(@args);
- $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
-}
-
-=head2 type
-
- Title : type
- Usage : $featuregroup->type($optional_arg);
- Function: get/set the type of the featuregroup
- Comments: this is probably going to be a string like
- "quality control", "mismatch blah blah", etc.
- Returns : the featuregroup type
- Args : a new value for the featuregroup type
-
-=cut
-
-sub type {
- my $self = shift;
- $self->{type} = shift if @_;
- return $self->{type};
-}
-
-=head2 id
-
- Title : id
- Usage : $featuregroup->id($optional_arg);
- Function: get/set the id of the featuregroup
- Returns : the featuregroup id
- Args : a new value for the featuregroup id
-
-=cut
-
-sub id {
- my $self = shift;
- $self->{id} = shift if @_;
- return $self->{id};
-}
-
-
-=head2 standard_deviation
-
- Title : standard_deviation
- Usage : $featuregroup->standard_deviation($optional_arg);
- Function: get/set the standard deviation of the featuregroup value
- Returns : the featuregroup standard deviation
- Args : a new value for the featuregroup standard deviation
- Notes : this method does no calculation, it merely holds a value
-
-=cut
-
-sub standard_deviation {
- my $self = shift;
- $self->{standard_deviation} = shift if @_;
- return $self->{standard_deviation};
-}
-
-=head2 quantitation
-
- Title : quantitation
- Usage : $featuregroup->quantitation($optional_arg);
- Function: get/set the quantitation of the featuregroup
- Returns : the featuregroup's quantitated value
- Args : a new value for the featuregroup's quantitated value
- Notes : this method does no calculation, it merely holds a value
-
-=cut
-
-sub quantitation {
- my $self = shift;
- $self->{quantitation} = shift if @_;
- return $self->{quantitation};
-}
-
-=head2 quantitation_units
-
- Title : quantitation_units
- Usage : $featuregroup->quantitation_units($optional_arg);
- Function: get/set the quantitation units of the featuregroup
- Returns : the featuregroup's quantitated value units
- Args : a new value for the featuregroup's quantitated value units
-
-=cut
-
-sub quantitation_units {
- my $self = shift;
- $self->{quantitation_units} = shift if @_;
- return $self->{quantitation_units};
-}
-
-=head2 presence
-
- Title : presence
- Usage : $featuregroup->presence($optional_arg);
- Function: get/set the presence call of the featuregroup
- Returns : the featuregroup's presence call
- Args : a new value for the featuregroup's presence call
-
-=cut
-
-sub presence {
- my $self = shift;
- $self->{presence} = shift if @_;
- return $self->{presence};
-}
-
-=head2 add_feature
-
- Title : add_feature
- Usage : $feature_copy = $featuregroup->add_feature($feature);
- Function: add a feature to the featuregroup
- Returns : see this_feature()
- Args : a Bio::Expression::FeatureI compliant object
-
-=cut
-
-sub add_feature {
- my($self,@args) = @_;
- foreach my $feature (@args){
- $self->throw('Features must be Bio::Expression::FeatureI compliant') unless $feature->isa('Bio::Expression::FeatureI');
- push @{$self->{features}}, $feature;
- }
-
- return $self->{features} ? $self->{features}->[-1] : undef;
-}
-
-=head2 this_feature
-
- Title : this_feature
- Usage : $feature = $featuregroup->this_feature
- Function: access the last feature added to the featuregroup
- Returns : the last feature added to the featuregroup
- Args : none
-
-=cut
-
-sub this_feature {
- my $self = shift;
- return $self->{features} ? $self->{features}->[-1] : undef;
-}
-
-=head2 each_feature
-
- Title : each_feature
- Usage : @features = $featuregroup->each_feature
- Function: returns a list of Bio::Expression::FeatureI compliant
- objects
- Returns : a list of objects
- Args : none
-
-=cut
-
-sub each_feature {
- my $self = shift;
- return @{$self->{features}};
-}
-
-=head2 each_feature_quantitation
-
- Title : each_feature_quantitation
- Usage : @featurequantitions = $featuregroup->each_feature_quantitation;
- Function: returns an list of quantitations of the features in the featuregroup
- Returns : a list of numeric values
- Args : none
-
-=cut
-
-sub each_feature_quantitation {
- my $self = shift;
- my @values = ();
- push @values, $_->value foreach $self->each_feature;
- return @values;
-}
-
-=head2 is_qc
-
- Title : is_qc
- Usage : $is_quality_control = $featuregroup->is_qc
- Function: get/set whether or not the featuregroup is used for quality control purposes
- Returns : a boolean (equivalent)
- Args : a new value
-
-=cut
-
-sub is_qc {
- my $self = shift;
- $self->{is_qc} = shift if defined @_;
- return $self->{is_qc};
-}
-
-1;
View
29 Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
@@ -1,29 +0,0 @@
-# Let the code begin...
-package Bio::Expression::FeatureGroup::FeatureGroupMas50;
-
-use strict;
-
-use base qw(Bio::Expression::FeatureGroup);
-use vars qw($DEBUG);
-
-use Class::MakeMethods::Emulator::MethodMaker
- get_set => [qw(
-
- probe_set_name stat_pairs stat_pairs_used
- signal detection detection_p-value
- stat_common_pairs signal_log_ratio
- signal_log_ratio_low
- signal_log_ratio_high change change_p-value
- positive negative pairs pairs_used
- pairs_inavg pos_fraction log_avg
- pos_neg avg_diff abs_call inc dec
- inc_ratio dec_ratio pos_change
- neg_change inc_dec dpos-dneg_ratio
- log_avg_ratio_change diff_call
- avg_diff_change b_a fold_change
- sort_score
-
- )],
-;
-
-1;
View
61 Bio/Expression/ProbeI.pm
@@ -1,61 +0,0 @@
-# $Id$
-# BioPerl module for Bio::Expression::ProbeI
-#
-# Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
-# Human Genetics, UCLA Medical School, University of California, Los Angeles
-
-# POD documentation - main docs before the code
-
-=head1 NAME
-
-Bio::Expression::ProbeI - an interface class for DNA/RNA probes
-
-=head1 SYNOPSIS
-
-Do not use this module directly
-
-=head1 DESCRIPTION
-
-This class ISA Bio::Expression::FeatureI, nothing more.
-
-=head1 FEEDBACK
-
-=head2 Mailing Lists
-
-User feedback is an integral part of the evolution of this and other
-Bioperl modules. Send your comments and suggestions preferably to one
-of the Bioperl mailing lists. Your participation is much appreciated.
-
- bioperl-l@bioperl.org - General discussion
- http://bioperl.org/MailList.shtml - About the mailing lists
-
-=head2 Reporting Bugs
-
-Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.
- Bug reports can be submitted via email or the web:
-
- bioperl-bugs@bio.perl.org
- http://bio.perl.org/bioperl-bugs/
-
-=head1 AUTHOR
-
-Allen Day E<lt>allenday@ucla.eduE<gt>
-
-=head1 APPENDIX
-
-The rest of the documentation details each of the object
-methods. Internal methods are usually preceded with a _
-
-=cut
-
-# Let the code begin...
-package Bio::Expression::ProbeI;
-
-use strict;
-use Bio::Root::Root;
-
-use base qw(Bio::Expression::FeatureI);
-use vars qw($DEBUG);
-
-1;
View
70 t/data/BK000016-tpa.gbk
@@ -1,70 +0,0 @@
-LOCUS BK000016 1162 bp mRNA linear ROD 17-MAY-2002
-DEFINITION TPA: Mus musculus pantothenate kinase 4 mRNA, partial cds.
-ACCESSION BK000016
-VERSION BK000016.1 GI:20043254
-KEYWORDS Third Party Annotation; TPA.
-SOURCE Mus musculus (house mouse)
- ORGANISM Mus musculus
- Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
- Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
-REFERENCE 1 (bases 1 to 1162)
- AUTHORS Zhou,B., Westaway,S.K., Levinson,B., Johnson,M.A., Gitschier,J. and
- Hayflick,S.J.
- TITLE A novel pantothenate kinase gene (PANK2) is defective in
- Hallervorden-Spatz syndrome
- JOURNAL Nat. Genet. 28 (4), 345-349 (2001)
- MEDLINE 21372465
- PUBMED 11479594
-REFERENCE 2 (bases 1 to 1162)
- AUTHORS Zhou,B., Westaway,S.K., Levinson,B., Johnson,M.A., Gitschier,J. and
- Hayflick,S.J.
- TITLE Direct Submission
- JOURNAL Submitted (31-JUL-2001) Medicine and HHMI, University of
- California, San Francisco, 3rd and Parnassus Avenues, San
- Francisco, CA 94143, USA
-PRIMARY TPA_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
- 1-455 BE554781.1 1-455
- 177-687 BG146074.1 1-511
- 608-956 AA671765.1 45-393
- 656-1162 BE982078.1 1-507 c
-FEATURES Location/Qualifiers
- source 1..1162
- /organism="Mus musculus"
- /mol_type="mRNA"
- /db_xref="taxon:10090"
- CDS <1..1119
- /note="PANK4"
- /codon_start=1
- /product="pantothenate kinase 4"
- /protein_id="DAA00010.1"
- /db_xref="GI:20043255"
- /translation="ERGASGGGSGGDSLDKSITLPPDEIFRNLENAKRFAIDIGGSLT
- KLAYYSTVQHKVAKVRSFDHPGKDVEQDHEPPYEISVQEEITARLHFIKFENTYMEAC
- LDFIRDHLVNTETKVIQATGGGAYKFKDLIEEKLRLKVDKEDVMTCLIKGCNFVLKNI
- PHEAFMYQKDADPEFRFQTNHPNIFPYLLVNIGSGVSIVKVETEDRFEWIGGSSIGGG
- TFWGLGALLTKTKKFDELLQLASRGRHANVDMLVQDIYGGAHQTLGLSGNLIASSFGK
- SATADREFSKEDMAKSLLHMISNDIGQLACLYAKLHGLDRVYFGGFFIRGHPVTMRTI
- TYSINFFSKGEVQALFLRHEGYLGAIGAFLKGAEQDSE"
-BASE COUNT 290 a 308 c 332 g 232 t
-ORIGIN
- 1 gagcgtggag cgagtggcgg cgggagcggc ggggacagtc tggacaagag catcacgctg
- 61 ccccccgacg agatcttccg caacctggag aacgccaagc gcttcgccat tgatataggt
- 121 ggatcattga ccaagttggc atactattcc accgtacagc acaaagtggc caaagtgaga
- 181 tcttttgacc acccgggaaa ggacgtggag caggatcatg agccacccta tgagatctca
- 241 gtccaggagg agatcacagc tcgcctgcat ttcatcaagt ttgagaatac ctacatggaa
- 301 gcctgcctgg acttcatcag agaccaccta gtcaacactg agaccaaggt catccaggcc
- 361 actgggggtg gagcctataa gttcaaggac ctcatcgagg aaaagctgcg tctgaaggtg
- 421 gacaaagagg atgtaatgac ctgcttgata aaggggtgca acttcgtgct gaagaacatc
- 481 ccgcatgagg ccttcatgta ccagaaagac gcagacccag agtttcgatt tcagacaaat
- 541 caccccaaca tcttccccta cctcctagtc aacattggct ctggcgtctc catcgtgaag
- 601 gtggagacag aggaccggtt tgagtggatt ggtggaagct ccattggagg aggcaccttc
- 661 tggggcctcg gggctctgct caccaaaaca aagaagtttg atgagctgct gcagctggct
- 721 tccagaggcc ggcatgccaa cgttgacatg ctggtccagg acatctatgg tggggcccac
- 781 cagaccctgg gcctgagtgg caatctcatc gcaagcagtt ttgggaagtc agccactgct
- 841 gacagagagt tctccaaaga agacatggcc aagagcctgc tgcacatgat cagcaatgac
- 901 atcgggcagc tcgcctgtct gtacgccaag ctccacggct tggacagggt ctactttggg
- 961 ggcttcttca tccggggtca ccccgtgacc atgcgcacaa tcacctacag cattaacttc
- 1021 ttctccaagg gtgaagtcca ggcactcttc ctgagacatg aaggctacct gggagccatc
- 1081 ggggcatttt taaaaggagc cgagcaagac agtgagtaga gtcactgctg tgagcagtgg
- 1141 ctggctgtgc aggacgcggc cg
-//
View
443 t/data/hsinsulin.blastcl3.blastn
@@ -1,443 +0,0 @@
-BLASTN 2.2.6 [Apr-09-2003]
-
-
-Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
-Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
-"Gapped BLAST and PSI-BLAST: a new generation of protein database search
-programs", Nucleic Acids Res. 25:3389-3402.
-
-Query= human
- (179 letters)
-
-Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
-or phase 0, 1 or 2 HTGS sequences)
- 1,787,533 sequences; -24,016,349 total letters
-
-Searching... please wait.. done
-
- Score E
-Sequences producing significant alignments: (bits) Value
-
-gb|J00265.1|HUMINS01 Human insulin gene, complete cds 355 2e-95
-emb|V00565.1|HSINSU Human gene for preproinsulin, from chromosom... 355 2e-95
-gb|M10039.1|HUMINSPR Human alpha-type insulin gene and 5' flanki... 355 2e-95
-gb|L15440.1|HUMINSTHIG Homo sapiens tyrosine hydroxylase (TH) ge... 355 2e-95
-gb|AC132217.15| Homo sapiens chromosome 11, clone RP11-889I17, c... 347 4e-93
-gb|AC130303.8| Homo sapiens chromosome 11, clone RP4-539G11, com... 347 4e-93
-gb|AY138590.1|AY138589S2 Homo sapiens insulin (INS) gene, exons ... 347 4e-93
-emb|AJ009655.1|HSA9655 Homo sapiens ins gene, partial 347 4e-93
-gb|AY137497.1|AY137496S2 Pan troglodytes insulin precursor (INS)... 339 9e-91
-emb|X61089.1|PTPPINS P.troglodytes gene for preproinsulin 315 1e-83
-gb|AY137500.1|AY137498S3 Gorilla gorilla insulin precursor (INS)... 262 2e-67
-gb|AY137503.1|AY137501S3 Pongo pygmaeus insulin precursor (INS) ... 222 1e-55
-emb|X61092.1|CEPPINS C.aethiops gene for preproinsulin 129 2e-27
-
->gb|J00265.1|HUMINS01 Human insulin gene, complete cds
- Length = 4044
-
- Score = 355 bits (179), Expect = 2e-95
- Identities = 179/179 (100%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2228 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 2287
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2288 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 2347
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2348 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 2406
-
-
->emb|V00565.1|HSINSU Human gene for preproinsulin, from chromosome 11. Includes a highly
- polymorphic region upstream from the insulin gene
- containing tandemly repeated sequences
- Length = 4992
-
- Score = 355 bits (179), Expect = 2e-95
- Identities = 179/179 (100%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2228 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 2287
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2288 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 2347
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2348 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 2406
-
-
->gb|M10039.1|HUMINSPR Human alpha-type insulin gene and 5' flanking polymorphic region
- Length = 3943
-
- Score = 355 bits (179), Expect = 2e-95
- Identities = 179/179 (100%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2503 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 2562
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2563 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 2622
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 2623 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 2681
-
-
->gb|L15440.1|HUMINSTHIG Homo sapiens tyrosine hydroxylase (TH) gene, 3' end; insulin (INS)
- gene, complete cds; insulin-like growth factor 2 (IGF2)
- gene, 5' end
- Length = 12565
-
- Score = 355 bits (179), Expect = 2e-95
- Identities = 179/179 (100%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 4289 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 4348
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 4349 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 4408
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 4409 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 4467
-
-
->gb|AC132217.15| Homo sapiens chromosome 11, clone RP11-889I17, complete sequence
- Length = 170027
-
- Score = 347 bits (175), Expect = 4e-93
- Identities = 178/179 (99%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
-Sbjct: 86461 gtctgttccaagggcctttgcgtcaggtgggctcaggattccagggtggctggaccccag 86520
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 86521 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 86580
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 86581 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 86639
-
-
->gb|AC130303.8| Homo sapiens chromosome 11, clone RP4-539G11, complete sequence
- Length = 171366
-
- Score = 347 bits (175), Expect = 4e-93
- Identities = 178/179 (99%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 127800 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 127859
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 127860 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 127919
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
-Sbjct: 127920 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtcacccag 127978
-
-
->gb|AY138590.1|AY138589S2 Homo sapiens insulin (INS) gene, exons 1, 2, 3, and complete cds;
- and insulin-like growth factor (IGF2) gene, exon 1
- Length = 4233
-
- Score = 347 bits (175), Expect = 4e-93
- Identities = 178/179 (99%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 378 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 437
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 438 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 497
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
-Sbjct: 498 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtcacccag 556
-
-
->emb|AJ009655.1|HSA9655 Homo sapiens ins gene, partial
- Length = 1393
-
- Score = 347 bits (175), Expect = 4e-93
- Identities = 178/179 (99%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 6 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 65
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 66 gccccagctgtgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 125
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 126 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 184
-
-
->gb|AY137497.1|AY137496S2 Pan troglodytes insulin precursor (INS) gene, complete cds
- Length = 4124
-
- Score = 339 bits (171), Expect = 9e-91
- Identities = 177/179 (98%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 338 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 397
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
-Sbjct: 398 gccccagctctgcagcagggaggacgtggctgggctcttgaagcatgtgggggtgagccc 457
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
-Sbjct: 458 aggggccccaaggcagggcacctggccttcagccggcctcagccctgcctgtctcccag 516
-
-
->emb|X61089.1|PTPPINS P.troglodytes gene for preproinsulin
- Length = 2483
-
- Score = 315 bits (159), Expect = 1e-83
- Identities = 175/179 (97%), Gaps = 1/179 (0%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 1028 gtctgttccaagggcctttgcgtcaggtgggctcagggttccagggtggctggaccccag 1087
-
-
-Query: 61 gccccagctctgcagcagggaggacgtggctgggctcgtgaagcatgtgggggtgagccc 120
- ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
-Sbjct: 1088 gccccagctctgcagcagggaggacgtggctgggctcttgaagcatgtgggggtgagccc 1147
-
-
-Query: 121 aggggccccaaggcagggcacctggccttcagcctgcctcagccctgcctgtctcccag 179
- |||||||||||||||||||| || |||||||||| ||||||||||||||||||||||||
-Sbjct: 1148 aggggccccaaggcagggcagct-gccttcagccggcctcagccctgcctgtctcccag 1205
-
-
->gb|AY137500.1|AY137498S3 Gorilla gorilla insulin precursor (INS) gene, complete cds
- Length = 4146
-
- Score = 262 bits (132), Expect = 2e-67
- Identities = 141/144 (97%)
- Strand = Plus / Plus
-
-
-Query: 36 gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 95
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 389 gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 448
-
-
-Query: 96 tcgtgaagcatgtgggggtgagcccaggggccccaaggcagggcacctggccttcagcct 155
- || |||||||||||||||||||||||||||||||||||||||||| |||||||||||||
-Sbjct: 449 tcttgaagcatgtgggggtgagcccaggggccccaaggcagggcaactggccttcagccg 508
-
-
-Query: 156 gcctcagccctgcctgtctcccag 179
- ||||||||||||||||||||||||
-Sbjct: 509 gcctcagccctgcctgtctcccag 532
-
-
->gb|AY137503.1|AY137501S3 Pongo pygmaeus insulin precursor (INS) gene, complete cds
- Length = 4126
-
- Score = 222 bits (112), Expect = 1e-55
- Identities = 136/144 (94%)
- Strand = Plus / Plus
-
-
-Query: 36 gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 95
- ||||||||||||||||||||||||||| ||||||||||||| ||||||||||||||||||
-Sbjct: 384 gggttccagggtggctggaccccaggctccagctctgcagctgggaggacgtggctgggc 443
-
-
-Query: 96 tcgtgaagcatgtgggggtgagcccaggggccccaaggcagggcacctggccttcagcct 155
- || |||||||| ||||||||||||||||||||||| |||||||||||||||||||||||
-Sbjct: 444 tcttgaagcatttgggggtgagcccaggggccccagggcagggcacctggccttcagccg 503
-
-
-Query: 156 gcctcagccctgcctgtctcccag 179
- ||||||| |||||||||||||||
-Sbjct: 504 acctcagctctgcctgtctcccag 527
-
-
->emb|X61092.1|CEPPINS C.aethiops gene for preproinsulin
- Length = 1909
-
- Score = 129 bits (65), Expect = 2e-27
- Identities = 86/93 (92%)
- Strand = Plus / Plus
-
-
-Query: 36 gggttccagggtggctggaccccaggccccagctctgcagcagggaggacgtggctgggc 95
- ||||||||||||||||||||||||||||||||||||||| |||||||||| |||||||||
-Sbjct: 514 gggttccagggtggctggaccccaggccccagctctgcaacagggaggacatggctgggc 573
-
-
-Query: 96 tcgtgaagcatgtgggggtgagcccaggggccc 128
- || |||||| | || |||||| |||||||||||
-Sbjct: 574 tcttgaagcgtttgagggtgaacccaggggccc 606
-
-
- Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
- or phase 0, 1 or 2 HTGS sequences)
- Posted date: Jul 31, 2003 1:26 AM
- Number of letters in database: 192,913,178
- Number of sequences in database: 1,867,771
-
-Lambda K H
- 1.37 0.711 0.00
-
-Gapped
-Lambda K H
- 1.37 0.711 7.29e-304
-
-
-Matrix: blastn matrix:1 -3
-Gap Penalties: Existence: 5, Extension: 2
-Number of Hits to DB: 1,670,626
-Number of Sequences: 1867771
-Number of extensions: 1670626
-Number of successful extensions: 118444
-Number of sequences better than 1.0e-20: 13
-Number of HSP's better than 0.0 without gapping: 13
-Number of HSP's successfully gapped in prelim test: 0
-Number of HSP's that attempted gapping in prelim test: 118410
-Number of HSP's gapped (non-prelim): 33
-length of query: 179
-length of database: 8,782,847,770
-effective HSP length: 20
-effective length of query: 159
-effective length of database: 8,745,492,350
-effective search space: 1390533283650
-effective search space used: 1390533283650
-T: 0
-A: 0
-X1: 6 (11.9 bits)
-X2: 15 (29.7 bits)
-S1: 12 (24.3 bits)
-S2: 54 (107.5 bits)
-
-Query= owlmonkey
- (180 letters)
-
-Searching... please wait.. done
-
- Score E
-Sequences producing significant alignments: (bits) Value
-
-gb|J02989.1|ATRINS Owl monkey (A.trivirgatus) insulin gene, comp... 357 4e-96
-
->gb|J02989.1|ATRINS Owl monkey (A.trivirgatus) insulin gene, complete cds
- Length = 2113
-
- Score = 357 bits (180), Expect = 4e-96
- Identities = 180/180 (100%)
- Strand = Plus / Plus
-
-
-Query: 1 gtctgttccaagggccttcgagccagtctgggccccagggctgccccactcggggttcca 60
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 551 gtctgttccaagggccttcgagccagtctgggccccagggctgccccactcggggttcca 610
-
-
-Query: 61 gagcagttggaccccaggtctcagcgggagggtgtggctgggctctgaagcatttgggtg 120
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 611 gagcagttggaccccaggtctcagcgggagggtgtggctgggctctgaagcatttgggtg 670
-
-
-Query: 121 agcccaggggctcagggcagggcacctgccttcagcggcctcagcctgcctgtctcccag 180
- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Sbjct: 671 agcccaggggctcagggcagggcacctgccttcagcggcctcagcctgcctgtctcccag 730
-
-
- Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
- or phase 0, 1 or 2 HTGS sequences)
- Posted date: Jul 31, 2003 1:26 AM
- Number of letters in database: 192,913,178
- Number of sequences in database: 1,867,771
-
-Lambda K H
- 1.37 0.711 0.00
-
-Gapped
-Lambda K H
- 1.37 0.711 7.29e-304
-
-
-Matrix: blastn matrix:1 -3
-Gap Penalties: Existence: 5, Extension: 2
-Number of Hits to DB: 910,717
-Number of Sequences: 1867771
-Number of extensions: 910717
-Number of successful extensions: 72147
-Number of sequences better than 1.0e-20: 1
-Number of HSP's better than 0.0 without gapping: 1
-Number of HSP's successfully gapped in prelim test: 0
-Number of HSP's that attempted gapping in prelim test: 72146
-Number of HSP's gapped (non-prelim): 1
-length of query: 180
-length of database: 8,782,847,770
-effective HSP length: 20
-effective length of query: 160
-effective length of database: 8,745,492,350
-effective search space: 1399278776000
-effective search space used: 1399278776000
-T: 0
-A: 0
-X1: 6 (11.9 bits)
-X2: 15 (29.7 bits)
-S1: 12 (24.3 bits)
-S2: 54 (107.5 bits)
Please sign in to comment.
Something went wrong with that request. Please try again.