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