1 2<a name="input.1"></a> 3<h3>Input files for usage example </h3> 4 5'tembl:x65923' is a sequence entry in the example nucleic acid database 'tembl' 6<p> 7<p><h3>Database entry: tembl:x65923</h3> 8<table width="90%"><tr><td bgcolor="#FFCCFF"> 9<pre> 10ID X65923; SV 1; linear; mRNA; STD; HUM; 518 BP. 11XX 12AC X65923; 13XX 14DT 13-MAY-1992 (Rel. 31, Created) 15DT 18-APR-2005 (Rel. 83, Last updated, Version 11) 16XX 17DE H.sapiens fau mRNA 18XX 19KW fau gene. 20XX 21OS Homo sapiens (human) 22OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; 23OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; 24OC Homo. 25XX 26RN [1] 27RP 1-518 28RA Michiels L.M.R.; 29RT ; 30RL Submitted (29-APR-1992) to the INSDC. 31RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry, 32RL Universiteisplein 1, 2610 Wilrijk, BELGIUM 33XX 34RN [2] 35RP 1-518 36RX PUBMED; 8395683. 37RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.; 38RT "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as 39RT an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus"; 40RL Oncogene 8(9):2537-2546(1993). 41XX 42DR Ensembl-Gn; ENSG00000149806; Homo_sapiens. 43DR Ensembl-Tr; ENST00000279259; Homo_sapiens. 44DR Ensembl-Tr; ENST00000434372; Homo_sapiens. 45DR Ensembl-Tr; ENST00000525297; Homo_sapiens. 46DR Ensembl-Tr; ENST00000526555; Homo_sapiens. 47DR Ensembl-Tr; ENST00000527548; Homo_sapiens. 48DR Ensembl-Tr; ENST00000529259; Homo_sapiens. 49DR Ensembl-Tr; ENST00000529639; Homo_sapiens. 50DR Ensembl-Tr; ENST00000531743; Homo_sapiens. 51XX 52FH Key Location/Qualifiers 53FH 54FT source 1..518 55FT /organism="Homo sapiens" 56FT /chromosome="11q" 57FT /map="13" 58FT /mol_type="mRNA" 59FT /clone_lib="cDNA" 60FT /clone="pUIA 631" 61FT /tissue_type="placenta" 62FT /db_xref="taxon:9606" 63FT misc_feature 57..278 64FT /note="ubiquitin like part" 65FT CDS 57..458 66FT /gene="fau" 67FT /db_xref="GDB:135476" 68FT /db_xref="GOA:P35544" 69FT /db_xref="GOA:P62861" 70FT /db_xref="H-InvDB:HIT000322806.14" 71FT /db_xref="HGNC:3597" 72FT /db_xref="InterPro:IPR000626" 73FT /db_xref="InterPro:IPR006846" 74FT /db_xref="InterPro:IPR019954" 75FT /db_xref="InterPro:IPR019955" 76FT /db_xref="InterPro:IPR019956" 77FT /db_xref="PDB:2L7R" 78FT /db_xref="UniProtKB/Swiss-Prot:P35544" 79FT /db_xref="UniProtKB/Swiss-Prot:P62861" 80FT /protein_id="CAA46716.1" 81FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG 82FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG 83FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS" 84FT misc_feature 98..102 85FT /note="nucleolar localization signal" 86FT misc_feature 279..458 87FT /note="S30 part" 88FT polyA_signal 484..489 89FT polyA_site 509 90XX 91SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other; 92 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60 93 agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120 94 cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180 95 tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240 96 tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300 97 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360 98 agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420 99 cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480 100 tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518 101// 102</pre> 103</td></tr></table><p> 104 105<a name="input.3"></a> 106<h3>Input files for usage example 3</h3> 107<p><h3>File: prev.comp</h3> 108<table width="90%"><tr><td bgcolor="#FFCCFF"> 109<pre> 110# 111# Output from 'compseq' 112# 113# The Expected frequencies are calculated on the (false) assumption that every 114# word has equal frequency. 115# 116# The input sequences are: 117# HSFAU 118 119 120Word size 3 121Total count 516 122 123# 124# Word Obs Count Obs Frequency Exp Frequency Obs/Exp Frequency 125# 126AAA 17 0.0329457 0.0156250 2.1085271 127AAC 5 0.0096899 0.0156250 0.6201550 128AAG 18 0.0348837 0.0156250 2.2325581 129AAT 4 0.0077519 0.0156250 0.4961240 130ACA 5 0.0096899 0.0156250 0.6201550 131ACC 6 0.0116279 0.0156250 0.7441860 132ACG 2 0.0038760 0.0156250 0.2480620 133ACT 7 0.0135659 0.0156250 0.8682171 134AGA 12 0.0232558 0.0156250 1.4883721 135AGC 7 0.0135659 0.0156250 0.8682171 136AGG 16 0.0310078 0.0156250 1.9844961 137AGT 10 0.0193798 0.0156250 1.2403101 138ATA 2 0.0038760 0.0156250 0.2480620 139ATC 3 0.0058140 0.0156250 0.3720930 140ATG 7 0.0135659 0.0156250 0.8682171 141ATT 2 0.0038760 0.0156250 0.2480620 142CAA 10 0.0193798 0.0156250 1.2403101 143CAC 6 0.0116279 0.0156250 0.7441860 144CAG 13 0.0251938 0.0156250 1.6124031 145CAT 5 0.0096899 0.0156250 0.6201550 146CCA 12 0.0232558 0.0156250 1.4883721 147CCC 13 0.0251938 0.0156250 1.6124031 148CCG 8 0.0155039 0.0156250 0.9922481 149CCT 10 0.0193798 0.0156250 1.2403101 150CGA 2 0.0038760 0.0156250 0.2480620 151CGC 10 0.0193798 0.0156250 1.2403101 152CGG 9 0.0174419 0.0156250 1.1162791 153CGT 4 0.0077519 0.0156250 0.4961240 154CTA 5 0.0096899 0.0156250 0.6201550 155CTC 11 0.0213178 0.0156250 1.3643411 156CTG 10 0.0193798 0.0156250 1.2403101 157CTT 11 0.0213178 0.0156250 1.3643411 158GAA 11 0.0213178 0.0156250 1.3643411 159GAC 6 0.0116279 0.0156250 0.7441860 160GAG 10 0.0193798 0.0156250 1.2403101 161GAT 4 0.0077519 0.0156250 0.4961240 162GCA 7 0.0135659 0.0156250 0.8682171 163GCC 18 0.0348837 0.0156250 2.2325581 164GCG 8 0.0155039 0.0156250 0.9922481 165GCT 10 0.0193798 0.0156250 1.2403101 166GGA 13 0.0251938 0.0156250 1.6124031 167GGC 17 0.0329457 0.0156250 2.1085271 168GGG 7 0.0135659 0.0156250 0.8682171 169GGT 9 0.0174419 0.0156250 1.1162791 170GTA 6 0.0116279 0.0156250 0.7441860 171GTC 9 0.0174419 0.0156250 1.1162791 172GTG 8 0.0155039 0.0156250 0.9922481 173GTT 5 0.0096899 0.0156250 0.6201550 174TAA 7 0.0135659 0.0156250 0.8682171 175TAC 3 0.0058140 0.0156250 0.3720930 176TAG 4 0.0077519 0.0156250 0.4961240 177TAT 1 0.0019380 0.0156250 0.1240310 178TCA 10 0.0193798 0.0156250 1.2403101 179TCC 6 0.0116279 0.0156250 0.7441860 180TCG 7 0.0135659 0.0156250 0.8682171 181TCT 10 0.0193798 0.0156250 1.2403101 182TGA 4 0.0077519 0.0156250 0.4961240 183TGC 9 0.0174419 0.0156250 1.1162791 184TGG 14 0.0271318 0.0156250 1.7364341 185TGT 5 0.0096899 0.0156250 0.6201550 186TTA 2 0.0038760 0.0156250 0.2480620 187TTC 10 0.0193798 0.0156250 1.2403101 188TTG 7 0.0135659 0.0156250 0.8682171 189TTT 7 0.0135659 0.0156250 0.8682171 190 191Other 0 0.0000000 0.0000000 10000000000.0000000 192</pre> 193</td></tr></table><p> 194