recoder

 

Function

Remove restriction sites but maintain the same translation

Description

recoder scans a given nucleotide sequence for restriction sites. It reports single base positions in the restriction pattern which when mutated remove the restriction site whilst maintaining the same translation (in frame 1 of the input sequence).

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'.

Usage

Here is a sample session with recoder


% 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

Command line arguments

   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

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


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

Input file format

recoder reads a normal nucleic acid sequence USA.

Input files for usage example

'tembl:hsfau' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:hsfau

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
//

Output file format

Output files for usage example

File: hsfau.recoder

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->G  
EcoRII      CCWGG          182       S.S    183      C->A  
EcoRII      CCWGG          182       S.S    183      C->T  
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  


Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
redataSearch REBASE for enzyme name, references, suppliers etc
remapDisplay a sequence with restriction cut sites, translation etc
restoverFinds restriction enzymes that produce a specific overhang
restrictFinds restriction enzyme cleavage sites
showseqDisplay a sequence with features, translation etc
silentSilent 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.

Author(s)

This application was written by Tim Carver (tcarver@hgmp.mrc.ac.uk)

History

Written (January 2001) - Tim Carver

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/

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments