📄 prettyseq.txt
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0 gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 1740 ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 1800 gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 1860 aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 1920 catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 1980 gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 2040 gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 2100 ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 2160 cctcgag 2167// You can specifiy a file of ranges to extract by giving the '-range' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-range @myfile'). The format of the range file is: * Comment lines start with '#' in the first column. * Comment lines and blank lines are ignored. * The line may start with white-space. * There are two positive (integer) numbers per line separated by one or more space or TAB characters. * The second number must be greater or equal to the first number. * There can be optional text after the two numbers to annotate the line. * White-space before or after the text is removed. An example range file is:# this is my set of ranges12 23 4 5 this is like 12-23, but smaller67 10348 interesting regionOutput file format Output files for usage example File: paamir.prettyseqPRETTYSEQ of PAAMIR from 1 to 2167 ---------|---------|---------|---------|---------|---------| 1 GGTACCGCTGGCCGAGCATCTGCTCGATCACCACCAGCCGGGCGACGGGAACTGCACGAT 60 ---------|---------|---------|---------|---------|---------| 61 CTACCTGGCGAGCCTGGAGCACGAGCGGGTTCGCTTCGTACGGCGCTGAGCGACAGTCAC 120 ---------|---------|---------|---------|---------|---------| 121 AGGAGAGGAAACGGatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg 180 1 M G S H Q E R P L I G L L F S E 16 ---------|---------|---------|---------|---------|---------| 181 aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg 240 17 T G V T A D I E R S H A Y G A L L A V E 36 ---------|---------|---------|---------|---------|---------| 241 agcaactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc 300 37 Q L N R E G G V G G R P I E T L S Q D P 56 ---------|---------|---------|---------|---------|---------| 301 ccggcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccgggggg 360 57 G G D P D R Y R L C A E D F I R N R G V 76 ---------|---------|---------|---------|---------|---------| 361 tacggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcg 420 77 R F L V G C Y M S H T R K A V M P V V E 96 ---------|---------|---------|---------|---------|---------| 421 agcgcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccga 480 97 R A D A L L C Y P T P Y E G F E Y S P N 116 ---------|---------|---------|---------|---------|---------| 481 acatcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctga 540 117 I V Y G G P A P N Q N S A P L A A Y L I 136 ---------|---------|---------|---------|---------|---------| 541 ttcgccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa 600 137 R H Y G E R V V F I G S D Y I Y P R E S 156 ---------|---------|---------|---------|---------|---------| 601 gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatct 660 157 N H V M R H L Y R Q H G G T V L E E I Y 176 ---------|---------|---------|---------|---------|---------| 661 acattccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccagg 720 177 I P L Y P S D D D L Q R A V E R I Y Q A 196 [Part of this file has been deleted for brevity] 1441 GCCGGTGGACGTGGTCTTCACCAGCATTTTCCAGAATGGCCACCACGACGAGATCGCTGC 1500 ---------|---------|---------|---------|---------|---------| 1501 GCTGCTCGCCGCCGGGACTCCGCGCACTACCCTGGTGGCGCTGGTGGAGTACGAAAGCCC 1560 ---------|---------|---------|---------|---------|---------| 1561 CGCGGTGCTCTCGCAGATCATCGAGCTGGAGTGCCACGGCGTGATCACCCAGCCGCTCGA 1620 ---------|---------|---------|---------|---------|---------| 1621 TGCCCACCGGGTGCTGCCTGTGCTGGTATCGGCGCGGCGCATCAGCGAGGAAATGGCGAA 1680 ---------|---------|---------|---------|---------|---------| 1681 GCTGAAGCAGAAGACCGAGCAGCTCCAGGACCGCATCGCCGGCCAGGCCCGGATCAACCA 1740 ---------|---------|---------|---------|---------|---------| 1741 GGCCAAGGTGTTGCTGATGCAGCGCCATGGCTGGGACGAGCGCGAGGCGCACCAGCACCT 1800 ---------|---------|---------|---------|---------|---------| 1801 GTCGCGGGAAGCGATGAAGCGGCGCGAGCCGATCCTGAAGATCGCTCAGGAGTTGCTGGG 1860 ---------|---------|---------|---------|---------|---------| 1861 AAACGAGCCGTCCGCCTGAGCGATCCGGGCCGACCAGAACAATAACAAGAGGGGTATCGT 1920 ---------|---------|---------|---------|---------|---------| 1921 CATCATGCTGGGACTGGTTCTGCTGTACGTTGGCGCGGTGCTGTTTCTCAATGCCGTCTG 1980 ---------|---------|---------|---------|---------|---------| 1981 GTTGCTGGGCAAGATCAGCGGTCGGGAGGTGGCGGTGATCAACTTCCTGGTCGGCGTGCT 2040 ---------|---------|---------|---------|---------|---------| 2041 GAGCGCCTGCGTCGCGTTCTACCTGATCTTTTCCGCAGCAGCCGGGCAGGGCTCGCTGAA 2100 ---------|---------|---------|---------|---------|---------| 2101 GGCCGGAGCGCTGACCCTGCTATTCGCTTTTACCTATCTGTGGGTGGCCGCCAACCAGTT 2160 ------- 2161 CCTCGAG 2167Data files The codon usage table is read by default from "Ehum.cut" in the 'data/CODONS' directory of the EMBOSS distribution. If the name of a codon usage file is specified on the command line, then this file will first be searched for in the current directory and then in the 'data/CODONS' directory of the EMBOSS distribution. EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA. To see the available EMBOSS data files, run:% embossdata -showall To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:% embossdata -fetch -file Exxx.dat Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata". The directories are searched in the following order: * . (your current directory) * .embossdata (under your current directory) * ~/ (your home directory) * ~/.embossdataNotes None.References None.Warnings None.Diagnostic Error Messages "Range outside length of sequence" - this is self explanatory. You should specify a range of sequences to translate that is within the length of the input sequence.Exit status It always exits with a status of 0.Known bugs None.See also Program name Description abiview Reads ABI file and display the trace backtranambig Back translate a protein sequence to ambiguous codons backtranseq Back translate a protein sequence cirdna Draws circular maps of DNA constructs coderet Extract CDS, mRNA and translations from feature tables lindna Draws linear maps of DNA constructs pepnet Displays proteins as a helical net pepwheel Shows protein sequences as helices plotorf Plot potential open reading frames prettyplot Displays aligned sequences, with colouring and boxing remap Display sequence with restriction sites, translation etc seealso Finds programs sharing group names showalign Displays a multiple sequence alignment showdb Displays information on the currently available databases showfeat Show features of a sequence showorf Pretty output of DNA translations showseq Display a sequence with features, translation etc sixpack Display a DNA sequence with 6-frame translation and ORFs textsearch Search sequence documentation. Slow, use SRS and Entrez! transeq Translate nucleic acid sequences showseq has more options for specifying various ways of displaying a sequence, with or without various ways of translating it.Author(s) Alan Bleasby (ajb ⌨️ 快捷键说明
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