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recoder |
Several restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. To find out whether the single point mutations found by 'recoder', introduce new restriction sites, 'silent' should be run on the original sequence. ('Silent' searches for silent point mutation sites which maintain the same translation.
The output for 'recoder' is similar to the format used by 'silent'.
% recoder Remove restriction sites but maintain the same translation Input sequence: tembl:hsfau Comma separated enzyme list [all]: EcoRII Output file [hsfau.recoder]: |
Go to the input files for this example
Go to the output files for this example
Mandatory qualifiers:
[-seq] sequence Nucleic acid sequence
-enzymes string Comma separated enzyme list
[-outf] outfile Results file name
Optional qualifiers: (none)
Advanced qualifiers:
-sshow boolean Display untranslated sequence
-tshow boolean Display translated sequence
Associated qualifiers:
"-seq" related qualifiers
-sbegin1 integer First base used
-send1 integer Last base used, def=seq length
-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
-sopenfile1 string Input filename
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outf" related qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for required and optional values
-debug boolean Write debug output to program.dbg
-acdlog boolean Write ACD processing log to program.acdlog
-acdpretty boolean Rewrite ACD file as program.acdpretty
-acdtable boolean Write HTML table of options
-verbose boolean Report some/full command line options
-help boolean Report command line options. 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 deaths
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| Mandatory qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-seq] (Parameter 1) |
Nucleic acid sequence | Readable sequence | Required |
| -enzymes | Comma separated enzyme list | Any string is accepted | all |
| [-outf] (Parameter 2) |
Results file name | Output file | <sequence>.recoder |
| Optional qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced qualifiers | Allowed values | Default | |
| -sshow | Display untranslated sequence | Boolean value Yes/No | No |
| -tshow | Display translated sequence | Boolean value Yes/No | No |
ID HSFAU standard; RNA; HUM; 518 BP.
XX
AC X65923;
XX
SV X65923.1
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 23-SEP-1993 (Rel. 37, Last updated, Version 10)
XX
DE H.sapiens fau mRNA
XX
KW fau gene.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN [1]
RP 1-518
RA Michiels L.M.R.;
RT ;
RL Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN [2]
RP 1-518
RX MEDLINE; 93368957.
RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8:2537-2546(1993).
XX
DR SWISS-PROT; P35544; UBIM_HUMAN.
DR SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /chromosome="11q"
FT /db_xref="taxon:9606"
FT /organism="Homo sapiens"
FT /tissue_type="placenta"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /map="13"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /db_xref="SWISS-PROT:P35544"
FT /db_xref="SWISS-PROT:Q05472"
FT /gene="fau"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT misc_feature 98..102
FT /note="nucleolar localization signal"
FT misc_feature 279..458
FT /note="S30 part"
FT polyA_signal 484..489
FT polyA_site 509
XX
SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518
//
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Results for HSFAU: KEY: Enzyme Enzyme name RS-Pattern Restriction enzyme recognition site pattern Match-Posn Position of the first base of RS pattern in sequence AA Amino acid. Original sequence(.)After mutation Base-Posn Position of base to be mutated in sequence Mutation The base mutation to perform Creating silent mutations Enzyme RS-Pattern Match-Posn AA Base-Posn Mutation EcoRII CCWGG 77 P.P 78 C->G EcoRII CCWGG 77 P.P 78 C->A EcoRII CCWGG 77 P.P 78 C->T EcoRII CCWGG 77 R.R 79 A->C EcoRII CCWGG 77 R.R 81 G->A EcoRII CCWGG 107 A.A 108 C->G EcoRII CCWGG 107 A.A 108 C->A EcoRII CCWGG 107 A.A 108 C->T EcoRII CCWGG 107 R.R 109 A->C EcoRII CCWGG 107 R.R 111 G->A EcoRII CCWGG 182 S.S 183 C->T EcoRII CCWGG 182 S.S 183 C->A EcoRII CCWGG 182 S.S 183 C->G EcoRII CCWGG 197 P.P 198 C->G EcoRII CCWGG 197 P.P 198 C->A EcoRII CCWGG 197 P.P 198 C->T EcoRII CCWGG 248 P.P 249 C->G EcoRII CCWGG 248 P.P 249 C->A EcoRII CCWGG 248 P.P 249 C->T EcoRII CCWGG 293 P.P 294 C->G EcoRII CCWGG 293 P.P 294 C->A EcoRII CCWGG 293 P.P 294 C->T Results for reverse of HSFAU: Creating silent mutations Enzyme RS-Pattern Match-Posn AA Base-Posn Mutation EcoRII CCWGG 77 P.P 79 T->G EcoRII CCWGG 77 P.P 79 T->C EcoRII CCWGG 107 P.P 109 T->G EcoRII CCWGG 107 P.P 109 T->C EcoRII CCWGG 182 P.P 184 A->G EcoRII CCWGG 182 P.P 184 A->C EcoRII CCWGG 197 P.P 199 A->G EcoRII CCWGG 197 P.P 199 A->C EcoRII CCWGG 248 P.P 250 A->G EcoRII CCWGG 248 P.P 250 A->C EcoRII CCWGG 293 P.P 295 A->C EcoRII CCWGG 293 P.P 295 A->G |
| Program name | Description |
|---|---|
| redata | Search REBASE for enzyme name, references, suppliers etc |
| remap | Display a sequence with restriction cut sites, translation etc |
| restover | Finds restriction enzymes that produce a specific overhang |
| restrict | Finds restriction enzyme cleavage sites |
| showseq | Display a sequence with features, translation etc |
| silent | Silent mutation restriction enzyme scan |
silent does the opposite to recoder. silent finds sites where a restriction enzyme site can be introduced without changing the translation in frame 1 of the sequence. recoder finds sites where a restriction enzyme site can be removed without changing the translation in frame 1 of the sequence.
Renamed from recode to recoder 16 May 2001 as the old name
clashed with a common UNIX print utility:
http://www.iro.umontreal.ca/contrib/recode/HTML/