wordcount Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Count and extract unique words in molecular sequence(s) Description wordcount counts and extracts all possible unique sequence words of a specified size in one or more DNA sequences. It writes an output file giving all possible words for that word size with a count of each word in the input sequences. Optionally, only words occuring a specified minimum number of times are reported. Usage Here is a sample session with wordcount % wordcount tembl:u68037 -wordsize=3 Count and extract unique words in molecular sequence(s) Output file [u68037.wordcount]: Go to the input files for this example Go to the output files for this example Command line arguments Count and extract unique words in molecular sequence(s) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Sequence(s) filename and optional format, or reference (input USA) -wordsize integer [@($(acdprotein)? 2 : 4)] Word size (Integer 1 or more) [-outfile] outfile [*.wordcount] Output file name Additional (Optional) qualifiers: -mincount integer [1] Minimum word count to report (Integer 1 or more) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format wordcount reads one or more nucleotide or protein sequnces. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Input files for usage example 'tembl:u68037' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:u68037 ID U68037; SV 1; linear; mRNA; STD; ROD; 1218 BP. XX AC U68037; XX DT 23-SEP-1996 (Rel. 49, Created) DT 04-MAR-2000 (Rel. 63, Last updated, Version 2) XX DE Rattus norvegicus EP1 prostanoid receptor mRNA, complete cds. XX KW . XX OS Rattus norvegicus (Norway rat) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; OC Muridae; Murinae; Rattus. XX RN [1] RP 1-1218 RA Abramovitz M., Boie Y.; RT "Cloning of the rat EP1 prostanoid receptor"; RL Unpublished. XX RN [2] RP 1-1218 RA Abramovitz M., Boie Y.; RT ; RL Submitted (26-AUG-1996) to the EMBL/GenBank/DDBJ databases. RL Biochemistry & Molecular Biology, Merck Frosst Center for Therapeutic RL Research, P. O. Box 1005, Pointe Claire - Dorval, Quebec H9R 4P8, Canada XX DR Ensembl-GO; ENSRNOESTG00000830631; Rattus_norvegicus. DR Ensembl-Gn; ENSRNOG00000004094; Rattus_norvegicus. DR Ensembl-Gn; ENSRNOG00000017743; Rattus_norvegicus. DR Ensembl-TO; ENSRNOESTT00000830623; Rattus_norvegicus. DR Ensembl-Tr; ENSRNOT00000005470; Rattus_norvegicus. DR Ensembl-Tr; ENSRNOT00000023860; Rattus_norvegicus. XX FH Key Location/Qualifiers FH FT source 1..1218 FT /organism="Rattus norvegicus" FT /strain="Sprague-Dawley" FT /mol_type="mRNA" FT /db_xref="taxon:10116" FT CDS 1..1218 FT /codon_start=1 FT /product="EP1 prostanoid receptor" FT /note="family 1 G-protein coupled receptor" FT /db_xref="GOA:P70597" FT /db_xref="InterPro:IPR000276" FT /db_xref="InterPro:IPR000708" FT /db_xref="InterPro:IPR001244" FT /db_xref="InterPro:IPR008365" FT /db_xref="InterPro:IPR017452" FT /db_xref="UniProtKB/Swiss-Prot:P70597" FT /protein_id="AAB07735.1" FT /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFSM FT TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTAG FT RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALALL FT AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAALV FT CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALRS FT SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLAV FT RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSRH FT SGFSHL" XX SQ Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other; atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc 60 agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg 120 cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc 180 caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc 240 agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg 300 tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc 360 ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt 420 gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta 480 gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac 540 tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg 600 cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca 660 ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc 720 tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga 780 ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc 840 agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc 900 cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg 960 gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta 1020 cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct 1080 atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg 1140 gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt 1200 ggcttcagcc acttgtga 1218 // Output file format Output files for usage example File: u68037.wordcount ctg 54 gcc 53 tgg 53 ggc 51 gct 47 cgc 47 gtg 40 tgc 39 cct 38 gcg 36 cca 29 ggg 26 tcc 25 ctt 25 cag 25 ccc 24 ggt 24 ctc 23 tgt 23 ccg 22 gca 22 cgt 22 cac 22 agc 21 ttg 19 acg 19 cgg 19 tcg 18 ttc 17 cat 17 agg 17 gag 16 act 16 gtc 16 aac 15 tct 14 atc 14 gga 14 tca 13 cta 13 atg 12 acc 11 gta 11 gtt 11 aca 10 tga 10 caa 10 tac 10 gac 9 tag 9 agt 9 ttt 8 cga 7 gat 6 taa 6 aga 5 tat 5 gaa 4 aat 3 tta 3 ata 3 att 3 aag 2 aaa 1 The file simply consists of two columns, separated by spaces or TAB characters. The first column consists of all the possible words of size wordsize. The second column consists of the count of those words in the input sequence. Data files None. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status 0 if successful. Known bugs None. See also Program name Description backtranambig Back-translate a protein sequence to ambiguous nucleotide sequence backtranseq Back-translate a protein sequence to a nucleotide sequence banana Plot bending and curvature data for B-DNA btwisted Calculate the twisting in a B-DNA sequence chaos Draw a chaos game representation plot for a nucleotide sequence compseq Calculate the composition of unique words in sequences dan Calculates nucleic acid melting temperature density Draw a nucleic acid density plot emowse Search protein sequences by digest fragment molecular weight freak Generate residue/base frequency table or plot isochore Plots isochores in DNA sequences mwcontam Find weights common to multiple molecular weights files mwfilter Filter noisy data from molecular weights file oddcomp Identify proteins with specified sequence word composition pepdigest Reports on protein proteolytic enzyme or reagent cleavage sites pepinfo Plot amino acid properties of a protein sequence in parallel pepstats Calculates statistics of protein properties Author(s) Ian Longden formerly at: Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Completed 27th November 1998. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None