eprop

 

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Function

Report propeptide cleavage sites in proteins

Description

ProP 1.0 server predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase (PC) prediction.

Usage

Here is a sample session with eprop 


% eprop 
Report propeptide cleavage sites in proteins
Input (aligned) protein sequence set: EDA_HUMAN.fsa
Output file [eda_human.eprop]:

Go to the input files for this example
Go to the output files for this example

Command line arguments 

Report propeptide cleavage sites in proteins
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) protein sequence set filename and
                                  optional format, or reference (input USA)
  [-outfile]           outfile    [*.eprop] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -plot               boolean    [N] Produce graphics
   -pcprediction       boolean    [N] Perform proprotein convertase prediction
   -signalp            boolean    [N] Include signal peptide cleavage site
                                  prediction

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)		 seqset (Aligned) protein sequence set filename and optional format, or reference (input USA) Readable set of sequences Required
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.eprop
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-plot boolean Produce graphics Boolean value Yes/No No
-pcprediction boolean Perform proprotein convertase prediction Boolean value Yes/No No
-signalp boolean Include signal peptide cleavage site prediction Boolean value Yes/No No
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1
-sbegin_sequence		 integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence		 integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence		 boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_sequence		 boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence		 boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-iquery1
-iquery_sequence		 string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence		 integer Input start position offset Any integer value 0
-sdbname1
-sdbname_sequence		 string Database name Any string  
-sid1
-sid_sequence		 string Entryname Any string  
-ufo1
-ufo_sequence		 string UFO features Any string  
-fformat1
-fformat_sequence		 string Features format Any string  
-fopenfile1
-fopenfile_sequence		 string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

eprop reads any normal sequence USAs.

Input files for usage example

File: EDA_HUMAN.fsa

>EDA_HUMAN   Q92838 Ectodysplasin A (Ectodermal dysplasia protein) (EDA protein). - Homo sapiens (Human).
MGYPEVERRELLPAAAPRERGSQGCGCGGAPARAGEGNSCLLFLGFFGLSLALHLLTLCC
YLELRSELRRERGAESRLGGSGTPGTSGTLSSLGGLDPDSPITSHLGQPSPKQQPLEPGE
AALHSDSQDGHQMALLNFFFPDEKPYSEEESRRVRRNKRSKSNEGADGPVKNKKKGKKAG
PPGPNGPPGPPGPPGPQGPPGIPGIPGIPGTTVMGPPGPPGPPGPQGPPGLQGPSGAADK
AGTRENQPAVVHLQGQGSAIQVKNDLSGGVLNDWSRITMNPKVFKLHPRSGELEVLVDGT
YFIYSQVEVYYINFTDFASYEVVVDEKPFLQCTRSIETGKTNYNTCYTAGVCLLKARQKI
AVKMVHADISINMSKHTTFFGAIRLGEAPAS

Output file format

Output files for usage example

File: eda_human.eprop



         ##### ProP v.1.0b ProPeptide Cleavage Site Prediction #####


         ##### Furin-type cleavage site prediction (Arginine/Lysine residues) #####


  391 EDA_HUMAN   
MGYPEVERRELLPAAAPRERGSQGCGCGGAPARAGEGNSCLLFLGFFGLSLALHLLTLCCYLELRSELRRERGAESRLGG      80
SGTPGTSGTLSSLGGLDPDSPITSHLGQPSPKQQPLEPGEAALHSDSQDGHQMALLNFFFPDEKPYSEEESRRVRRNKRS     160
KSNEGADGPVKNKKKGKKAGPPGPNGPPGPPGPPGPQGPPGIPGIPGIPGTTVMGPPGPPGPPGPQGPPGLQGPSGAADK     240
AGTRENQPAVVHLQGQGSAIQVKNDLSGGVLNDWSRITMNPKVFKLHPRSGELEVLVDGTYFIYSQVEVYYINFTDFASY     320
EVVVDEKPFLQCTRSIETGKTNYNTCYTAGVCLLKARQKIAVKMVHADISINMSKHTTFFGAIRLGEAPAS              400
................................................................................      80
..............................................................................P.     160
................................................................................     240
................................................................................     320
.......................................................................              400
 
Propeptide cleavage sites predicted:	Arg(R)/Lys(K): 1




Name           Pos    Context     Score  Pred
____________________________v_________________
EDA_HUMAN        8    GYPEVER|RE  0.057    .
EDA_HUMAN        9    YPEVERR|EL  0.128    .
EDA_HUMAN       18    LPAAAPR|ER  0.135    .
EDA_HUMAN       20    AAAPRER|GS  0.102    .
EDA_HUMAN       33    CGGAPAR|AG  0.090    .
EDA_HUMAN       65    CCYLELR|SE  0.089    .
EDA_HUMAN       69    ELRSELR|RE  0.081    .
EDA_HUMAN       70    LRSELRR|ER  0.195    .
EDA_HUMAN       72    SELRRER|GA  0.293    .
EDA_HUMAN       77    ERGAESR|LG  0.112    .
EDA_HUMAN      112    LGQPSPK|QQ  0.064    .
EDA_HUMAN      144    FFFPDEK|PY  0.060    .
EDA_HUMAN      152    YSEEESR|RV  0.096    .
EDA_HUMAN      153    SEEESRR|VR  0.114    .
EDA_HUMAN      155    EESRRVR|RN  0.204    .
EDA_HUMAN      156    ESRRVRR|NK  0.482    .
EDA_HUMAN      158    RRVRRNK|RS  0.182    .
EDA_HUMAN      159    RVRRNKR|SK  0.819 *ProP*
EDA_HUMAN      161    RRNKRSK|SN  0.131    .
EDA_HUMAN      171    GADGPVK|NK  0.060    .
EDA_HUMAN      173    DGPVKNK|KK  0.066    .
EDA_HUMAN      174    GPVKNKK|KG  0.119    .
EDA_HUMAN      175    PVKNKKK|GK  0.156    .
EDA_HUMAN      177    KNKKKGK|KA  0.116    .
EDA_HUMAN      178    NKKKGKK|AG  0.120    .
EDA_HUMAN      240    PSGAADK|AG  0.060    .
EDA_HUMAN      244    ADKAGTR|EN  0.082    .
EDA_HUMAN      263    GSAIQVK|ND  0.066    .
EDA_HUMAN      276    VLNDWSR|IT  0.077    .
EDA_HUMAN      282    RITMNPK|VF  0.057    .
EDA_HUMAN      285    MNPKVFK|LH  0.064    .
EDA_HUMAN      289    VFKLHPR|SG  0.116    .
EDA_HUMAN      327    EVVVDEK|PF  0.060    .
EDA_HUMAN      334    PFLQCTR|SI  0.152    .
EDA_HUMAN      340    RSIETGK|TN  0.061    .
EDA_HUMAN      355    AGVCLLK|AR  0.059    .
EDA_HUMAN      357    VCLLKAR|QK  0.099    .
EDA_HUMAN      359    LLKARQK|IA  0.073    .
EDA_HUMAN      363    RQKIAVK|MV  0.078    .
EDA_HUMAN      375    ISINMSK|HT  0.067    .
EDA_HUMAN      384    TFFGAIR|LG  0.076    .
____________________________^_________________

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 name Description
enetnglyc Report N-glycosylation sites in human proteins
enetoglyc Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
enetphos Report Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
esignalp Report protein signal cleavage sites
eyinoyang Report O-(beta)-GlcNAc attachment sites

Author(s)

This program is an EMBOSS wrapper for a program written by the CBS group http://www.cbs.dtu.dk/index.shtml

The original CBS group application must be licensed and installed to use this wrapper.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

None