\u4f7f\u7528\u4e09\u4ee3\u6d4b\u5e8f\u6570\u636e\u80fd\u83b7\u5f97\u8f83\u597d\u7684\u3001\u751a\u81f3\u5b8c\u6574\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002\u901a\u8fc7\u68c0\u6d4b\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e24\u7aef\u7684\u5c5e\u4e8e\u7aef\u7c92\uff08Telomere\uff09\u7684\u7279\u5b9a\u7684\u91cd\u590d\u5e8f\u5217\uff0c\u53ef\u4ee5\u77e5\u9053\u57fa\u56e0\u7ec4\u7ec4\u88c5\u662f\u5426\u5f97\u5230\u5b8c\u6574\u7684\u67d3\u8272\u4f53\u6c34\u5e73\u7684\u5e8f\u5217\u3002\u82e5\u5728\u5e8f\u5217\u4e2d\u95f4\u68c0\u6d4b\u5230\u7aef\u7c92\u5e8f\u5217\uff0c\u53ef\u4ee5\u77e5\u9053\u57fa\u56e0\u7ec4\u7ec4\u88c5\u8fc7\u7a0b\u4e2d\u5bf9Contigs\u6709\u9519\u8bef\u7684\u8fde\u63a5\u3002<\/p>\n\n\n\n
\u5728\u67d3\u8272\u4f53\u5e8f\u5217\u9996\u5c3e\u5b58\u5728\u7aef\u7c92\u5e8f\u5217\u3002\u5728\u4eba\u7c7b\u4e2d\uff0c\u7aef\u7c92\u5e8f\u5217\u7531\u91cd\u590d\u5355\u5143TTAGGG\uff0c\u4e32\u8054\u91cd\u590d\u7ea62500\u6b21\u7ec4\u6210\u3002<\/a> \u4e0d\u540c\u7684\u7269\u79cd\uff0c\u7aef\u7c92\u7684\u91cd\u590d\u5355\u5143\u53ef\u80fd\u4e0d\u4e00\u6837\uff0c\u53ef\u4ee5\u5728\u7aef\u7c92\u6570\u636e\u5e93<\/a>\u4e2d\u67e5\u8be2\u3002 \u6211\u5bf9\u4e00\u79cd\u5b50\u56ca\u83cc\u4f7f\u7528PacBio\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u4e86\u57fa\u56e0\u7ec4\u7ec4\u88c5\uff0c\u5f97\u523012\u6761\u5e8f\u5217\uff0c\u53d1\u73b0\u5927\u90e8\u5206\u5e8f\u5217\u9996\u5c3e\u5747\u51fa\u73b0\u4e86TTAGGG\/CCCTAA\u7684\u4e32\u8054\u91cd\u590d\u5e8f\u5217\u3002\u6211\u5bf9\u4e00\u79cd\u6606\u866b\u7269\u79cdPacBio\u7ec4\u88c5\u57fa\u56e0\u7ec4\u5e8f\u5217\u8fdb\u884c\u5206\u6790\uff0c\u53d1\u73b0\u5e8f\u5217\u9996\u5c3e\u51fa\u73b0\u4e00\u4e9b\u957f\u5ea6\u8f83\u957f\u5fae\u536b\u661f\u91cd\u590d\u5e8f\u5217\uff0c\u800c\u6ca1\u6709\u56fa\u5b9a\u7684\u91cd\u590d\u5355\u5143\uff0c\u8fd9\u548c\u7aef\u7c92\u6570\u636e\u5e93\u4e2d\u7684\u7ed3\u679c\u4e00\u81f4\u3002<\/p>\n\n\n\n \u7f16\u5199Perl\u7a0b\u5e8f\u5bf9\u5168\u57fa\u56e0\u7ec4\u5e8f\u5217\u7684\u7aef\u7c92\u5e8f\u5217\u8fdb\u884c\u641c\u7d22\uff0c\u67e5\u770b\u57fa\u56e0\u7ec4\u5e8f\u5217\u7684\u5b8c\u6574\u60c5\u51b5\uff1a<\/p>\n\n\n\n \u4f7f\u7528\u4e09\u4ee3\u6d4b\u5e8f\u6570\u636e\u80fd\u83b7\u5f97\u8f83\u597d\u7684\u3001\u751a\u81f3\u5b8c\u6574\u7684\u57fa\u56e0\u7ec4\u5e8f\u5217\u3002\u901a\u8fc7\u68c0\u6d4b\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e24\u7aef\u7684\u5c5e\u4e8e … \u7ee7\u7eed\u9605\u8bfb #!\/usr\/bin\/perl\nuse strict;\nuse Getopt::Long;\n\nmy $usage = <<USAGE;\nUsage:\n $0 genome.fasta > telomere_info.txt\n\n \u5927\u90e8\u5206\u7269\u79cd\u7aef\u7c92\u5e8f\u5217\u7684\u91cd\u590d\u5355\u5143\u662fTTAGGG\/CCCTAA\u3002\u672c\u7a0b\u5e8f\u80fd\u5728\u57fa\u56e0\u7ec4\u4e2d\u5bfb\u627e\u7aef\u7c92\u91cd\u590d\u5355\u5143\u7684\u4e32\u8054\u91cd\u590d\u5e8f\u5217\uff0c\u5e76\u7ed9\u51fa\u4f4d\u70b9\u4fe1\u606f\u3002\n\n --split-length <int> default: 100000\n --overlap-length <int> default: 10000\n \u7a0b\u5e8f\u4f1a\u5c06\u6bcf\u6761\u5e8f\u5217\u6253\u65ad\u540e\u8fdb\u884c\u91cd\u590d\u5355\u5143\u641c\u7d22\u3002\u8fd9\u4e24\u4e2a\u53c2\u6570\u8bbe\u7f6e\u6253\u65ad\u7684\u5e8f\u5217\u957f\u5ea6\u548c\u76f8\u90bb\u4e24\u5e8f\u5217\u4e4b\u95f4\u7684\u91cd\u53e0\u957f\u5ea6\u3002\n\n --repeat-unit <string> default: TTAGGG\n \u8bbe\u7f6e\u91cd\u590d\u5355\u5143\u78b1\u57fa\u5e8f\u5217\uff0c\u8be5\u91cd\u590d\u5355\u5143\u7684\u53cd\u5411\u4e92\u8865\u4e5f\u5c06\u4f5c\u4e3a\u91cd\u590d\u5355\u5143\u8fdb\u884c\u641c\u7d22\u3002\u53ef\u4ee5\u5728\u7aef\u7c92\u6570\u636e\u5e93\uff08http:\/\/telomerase.asu.edu\/sequences_telomere.html\uff09\u4e2d\u5bfb\u627e\u76ee\u6807\u7aef\u7c92\u91cd\u590d\u5355\u5143\u3002\n vertebrate sp. TTAGGG\n plants sp. TTTAGGG\n Pezizomycotina TTAGGG\n\n --min-repeat-num <int> default: 4\n \u8bbe\u7f6e\u91cd\u590d\u5355\u5143\u6700\u5c0f\u91cd\u590d\u6b21\u6570\u3002\n\n\nUSAGE\nif (@ARGV==0){die $usage}\n\nmy ($splitLength, $overlapLength, $repeatunit, $minRepeatNum);\nGetOptions(\n \"split-length:i\" => \\$splitLength,\n \"overlap-length:i\" => \\$overlapLength,\n \"repeat-unit:s\" => \\$repeatunit,\n \"min-repeat-num:s\" => \\$minRepeatNum,\n);\n$splitLength ||= 100000;\n$overlapLength ||= 10000;\n$repeatunit ||= \"TTAGGG\";\n$repeatunit = uc($repeatunit);\nmy $repeatunit_reverse = reverse $repeatunit;\n$repeatunit_reverse =~ tr\/ATCG\/TAGC\/;\n$minRepeatNum ||= 4;\n\n# \u8bfb\u53d6\u57fa\u56e0\u7ec4\u5e8f\u5217\nopen IN, $ARGV[0] or die \"Can not open file $ARGV[0], $!\\n\";\nmy (%seq, $seq_id);\nwhile (<IN>) {\n chomp;\n if (m\/^>(\\S+)\/) {\n $seq_id = $1;\n }\n else {\n $_ = uc($_);\n $seq{$seq_id} .= $_;\n }\n}\nclose IN;\n\n# \u5c06\u57fa\u56e0\u7ec4\u5e8f\u5217\u6253\u65ad\nmy (%seq_split, %seq_length);\nforeach my $id (keys %seq) {\n my $seq = $seq{$id};\n my $length = length($seq);\n $seq_length{$id} = $length;\n my $pos = 0;\n while ($pos < $length) {\n $seq_split{$id}{$pos} = substr($seq, $pos, $splitLength + $overlapLength);\n $pos += $splitLength;\n }\n}\n\nprint \"SeqID\\tSeqLength\\tStart\\tEnd\\tLength\\tType\\n\";\nforeach my $id (sort keys %seq_split) {\n foreach my $pos (sort {$a <=> $b} keys %{$seq_split{$id}}) {\n my $seq = $seq_split{$id}{$pos};\n while ($seq =~ m\/(($repeatunit){$minRepeatNum,})\/g) {\n my $length = length($1);\n my $end = pos($seq);\n $end = $end + $pos;\n my $start = $end - $length + 1;\n print \"$id\\t$seq_length{$id}\\t$start\\t$end\\t$length\\t$repeatunit\\n\";\n }\n while ($seq =~ m\/(($repeatunit_reverse){$minRepeatNum,})\/g) {\n my $length = length($1);\n my $end = pos($seq);\n $end = $end + $pos;\n my $start = $end - $length + 1;\n print \"$id\\t$seq_length{$id}\\t$start\\t$end\\t$length\\t$repeatunit_reverse\\n\";\n }\n }\n}\n<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"