newcpgseek.txt

emboss的linux版本的源代码

                                newcpgseek 



Function

   Reports CpG rich regions

Description

   newcpgseek reports CpG rich regions of a sequence as candidate CpG
   islands.

   CpG refers to a C nucleotide immediately followed by a G. The 'p' in
   'CpG' refers to the phosphate group linking the two bases.

   Detection of regions of genomic sequences that are rich in the CpG
   pattern is important because such regions are resistant to methylation
   and tend to be associated with genes which are frequently switched on.
   Regions rich in the CpG pattern are known as CpG islands.

   It has been estimated that about half of all mammalian genes have a
   CpG-rich region around their 5' end. It is said that all mammalian
   house-keeping genes have a CpG island!

   Non-mammalian vertebrates have some CpG islands that are associated
   with genes, but the association gets equivocal in the farther
   taxonomic groups.

   Finding a CpG island upstream of predicted exons or genes is good
   contributory evidence.

   CpG islands are usually defined as "length over 200bp with %GC over
   50% and obs/ervedexpexted CpG more than 0.6". However this program
   uses a running sum rather than a window to produce a score: if there
   is not a CpG at position i, then decrement runSum counter, but if CpG
   then runSum += CPGSCORE. Spans above the threshold are searched for
   recursively. If the score is higher than a threshold (17 at the
   moment) then a putative island is declared.

   This program reads in one or more sequences and finds regions where
   there is a high absolute frequency of CpG dimers as well as a high
   proportion of CpG compared to GpC.

Usage

   Here is a sample session with newcpgseek


% newcpgseek 
Reports CpG rich regions
Input nucleotide sequence(s): tembl:rnu68037
CpG score [17]: 
Output file [rnu68037.newcpgseek]: 

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

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
   -score              integer    [17] CpG score (Integer from 1 to 200)
  [-outfile]           outfile    [*.newcpgseek] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   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
   -sformat1           string     Input sequence format
   -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 standard output
   -filter             boolean    Read standard input, write 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. 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

Input file format

   newcpgseek reads a nucleic acid sequence USA.

  Input files for usage example

   'tembl:rnu68037' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:rnu68037

ID   RNU68037   standard; RNA; ROD; 1218 BP.
XX
AC   U68037;
XX
SV   U68037.1
XX
DT   23-SEP-1996 (Rel. 49, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 2)
XX
DE   Rattus norvegicus EP1 prostanoid receptor mRNA, complete cds.
XX
KW   .
XX
OS   Rattus norvegicus (Norway rat)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus.
XX
RN   [1]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   "Cloning of the rat EP1 prostanoid receptor";
RL   Unpublished.
XX
RN   [2]
RP   1-1218
RA   Abramovitz M., Boie Y.;
RT   ;
RL   Submitted (26-AUG-1996) to the EMBL/GenBank/DDBJ databases.
RL   Biochemistry & Molecular Biology, Merck Frosst Center for Therapeutic
RL   Research, P. O. Box 1005, Pointe Claire - Dorval, Quebec H9R 4P8, Canada
XX
DR   SWISS-PROT; P70597; PE21_RAT.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1218
FT                   /db_xref="taxon:10116"
FT                   /organism="Rattus norvegicus"
FT                   /strain="Sprague-Dawley"
FT   CDS             1..1218
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:P70597"
FT                   /note="family 1 G-protein coupled receptor"
FT                   /product="EP1 prostanoid receptor"
FT                   /protein_id="AAB07735.1"
FT                   /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFS
M
FT                   TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTA
G
FT                   RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALAL
L
FT                   AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAAL
V
FT                   CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALR
S
FT                   SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLA
V
FT                   RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSR
H
FT                   SGFSHL"
XX
SQ   Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other;
     atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc        6
0
     agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg       12
0
     cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc       18
0
     caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc       24
0
     agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg       30
0
     tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc       36
0
     ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt       42
0
     gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta       48
0
     gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac       54
0
     tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg       60
0
     cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca       66
0
     ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc       72
0
     tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga       78
0
     ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc       84
0
     agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc       90
0
     cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg       96
0
     gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta      102
0
     cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct      108
0
     atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg      114
0
     gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt      120
0
     ggcttcagcc acttgtga                                                    121
8
//

Output file format

  Output files for usage example

  File: rnu68037.newcpgseek



NEWCPGSEEK of RNU68037 from 1 to 1218
with score > 17

 Begin    End  Score        CpG  %CG  CG/GC
*    96   1032   630         87  66.1   0.65
  1072   1100    26          3  62.1   0.00
  1183   1193    26          2  72.7   2.00
-------------------------------------------

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                        Description
   cpgplot      Plot CpG rich areas
   cpgreport    Reports all CpG rich regions
   geecee       Calculates fractional GC content of nucleic acid sequences
   newcpgreport Report CpG rich areas

   As there is no official definition of what is a cpg island is, and
   worst where they begin and end, we have to live with 2 definitions and
   thus two methods. These are:

   1. newcpgseek and cpgreport - both declare a putative island if the
   score is higher than a threshold (17 at the moment). They now also
   displaying the actual CpG count, the % CG and the observed/expected
   ration in the region where the score is above the threshold. This
   scoring method based on sum/frequencies overpredicts islands but finds
   the smaller ones around primary exons. newcpgseek uses the same method
   as cpgreport but the output is different and more readable.

   2. newcpgreport and cpgplot use a sliding window within which the
   Obs/Exp ratio of CpG is calculated. The important thing to note in
   this method is that an island, in order to be reported, is defined as
   a region that satisfies the following contraints:

   Obs/Exp ratio > 0.6
   % C + % G > 50%
   Length > 200.

   For all practical purposes you should probably use newcpgreport. It is
   actually used to produce the human cpgisland database you can find on
   the EBI's ftp server as well as on the EBI's SRS server.

   geecee measures CG content in the entire input sequence and is not to
   be used to detect CpG islands. It can be usefull for detecting
   sequences that MIGHT contain an island.

Author(s)

   Rodrigo Lopez (rls