newcpgseek Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Identify and report CpG-rich regions in nucleotide sequence(s) Description newcpgseek identifies in a nucleotide sequence regions with higher than expected frequency of the dinucleotide CG. Each position in the sequence is scored using a running sum calculated from all positions in the sequence. This is a different method to that typically used for identifying CpG islands, for example by newcpgreport and cpgplot. This method overpredicts islands but finds the smaller ones around primary exons. An output file is written with information on the CpG-rich regions that are found. A feature table of sequence features in these regions is also written. Algorithm newcpgseek scores each position in the sequence using a running sum calculated from all positions in the sequence, starting with the first and ending in the last. If there is not a CG dinucleotide at a position, the score is decremented, if there is one, the score is incremented by a constant (user-defined) value. If the score for a region in the sequence is higher than a threshold (17 at the moment) then a putative island is declared. Sequence regions scoring above the threshold are searched for recursively. Usage Here is a sample session with newcpgseek % newcpgseek Identify and report CpG-rich regions in nucleotide sequence(s) Input nucleotide sequence(s): tembl:u68037 CpG score [17]: Output file [u68037.newcpgseek]: Go to the input files for this example Go to the output files for this example Command line arguments Identify and report CpG-rich regions in nucleotide sequence(s) Version: EMBOSS:6.4.0.0 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 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 Input file format newcpgseek reads one or more nucleotide sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Input files for usage example 'tembl:u68037' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:u68037 ID U68037; SV 1; linear; mRNA; STD; ROD; 1218 BP. XX AC U68037; 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; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; OC 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 Ensembl-GO; ENSRNOESTG00000830631; Rattus_norvegicus. DR Ensembl-Gn; ENSRNOG00000004094; Rattus_norvegicus. DR Ensembl-Gn; ENSRNOG00000017743; Rattus_norvegicus. DR Ensembl-TO; ENSRNOESTT00000830623; Rattus_norvegicus. DR Ensembl-Tr; ENSRNOT00000005470; Rattus_norvegicus. DR Ensembl-Tr; ENSRNOT00000023860; Rattus_norvegicus. XX FH Key Location/Qualifiers FH FT source 1..1218 FT /organism="Rattus norvegicus" FT /strain="Sprague-Dawley" FT /mol_type="mRNA" FT /db_xref="taxon:10116" FT CDS 1..1218 FT /codon_start=1 FT /product="EP1 prostanoid receptor" FT /note="family 1 G-protein coupled receptor" FT /db_xref="GOA:P70597" FT /db_xref="InterPro:IPR000276" FT /db_xref="InterPro:IPR000708" FT /db_xref="InterPro:IPR001244" FT /db_xref="InterPro:IPR008365" FT /db_xref="InterPro:IPR017452" FT /db_xref="UniProtKB/Swiss-Prot:P70597" FT /protein_id="AAB07735.1" FT /translation="MSPYGLNLSLVDEATTCVTPRVPNTSVVLPTGGNGTSPALPIFSM FT TLGAVSNVLALALLAQVAGRLRRRRSTATFLLFVASLLAIDLAGHVIPGALVLRLYTAG FT RAPAGGACHFLGGCMVFFGLCPLLLGCGMAVERCVGVTQPLIHAARVSVARARLALALL FT AAMALAVALLPLVHVGHYELQYPGTWCFISLGPPGGWRQALLAGLFAGLGLAALLAALV FT CNTLSGLALLRARWRRRRSRRFRENAGPDDRRRWGSRGLRLASASSASSITSTTAALRS FT SRGGGSARRVHAHDVEMVGQLVGIMVVSCICWSPLLVLVVLAIGGWNSNSLQRPLFLAV FT RLASWNQILDPWVYILLRQAMLRQLLRLLPLRVSAKGGPTELSLTKSAWEASSLRSSRH FT SGFSHL" XX SQ Sequence 1218 BP; 162 A; 397 C; 387 G; 272 T; 0 other; atgagcccct acgggcttaa cctgagccta gtggatgagg caacaacgtg tgtaacaccc 60 agggtcccca atacatctgt ggtgctgcca acaggcggta acggcacatc accagcgctg 120 cctatcttct ccatgacgct gggtgctgtg tccaacgtgc tggcgctggc gctgctggcc 180 caggttgcag gcagactgcg gcgccgccgc tcgactgcca ccttcctgtt gttcgtcgcc 240 agcctgcttg ccatcgacct agcaggccat gtgatcccgg gcgccttggt gcttcgcctg 300 tatactgcag gacgtgcgcc cgctggcggg gcctgtcatt tcctgggcgg ctgtatggtc 360 ttctttggcc tgtgcccact tttgcttggc tgtggcatgg ccgtggagcg ctgcgtgggt 420 gtcacgcagc cgctgatcca cgcggcgcgc gtgtccgtag cccgcgcacg cctggcacta 480 gccctgctgg ccgccatggc tttggcagtg gcgctgctgc cactagtgca cgtgggtcac 540 tacgagctac agtaccctgg cacttggtgt ttcattagcc ttgggcctcc tggaggttgg 600 cgccaggcgt tgcttgcggg cctcttcgcc ggccttggcc tggctgcgct ccttgccgca 660 ctagtgtgta atacgctcag cggcctggcg ctccttcgtg cccgctggag gcggcgtcgc 720 tctcgacgtt tccgagagaa cgcaggtccc gatgatcgcc ggcgctgggg gtcccgtgga 780 ctccgcttgg cctccgcctc gtctgcgtca tccatcactt caaccacagc tgccctccgc 840 agctctcggg gaggcggctc cgcgcgcagg gttcacgcac acgacgtgga aatggtgggc 900 cagctcgtgg gcatcatggt ggtgtcgtgc atctgctgga gccccctgct ggtattggtg 960 gtgttggcca tcgggggctg gaactctaac tccctgcagc ggccgctctt tctggctgta 1020 cgcctcgcgt cgtggaacca gatcctggac ccatgggtgt acatcctgct gcgccaggct 1080 atgctgcgcc aacttcttcg cctcctaccc ctgagggtta gtgccaaggg tggtccaacg 1140 gagctgagcc taaccaagag tgcctgggag gccagttcac tgcgtagctc ccggcacagt 1200 ggcttcagcc acttgtga 1218 // Output file format Output files for usage example File: u68037.newcpgseek NEWCPGSEEK of U68037 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 "CpG" refers to a C nucleotide immediately followed by a G. The 'p' in 'CpG' refers to the phosphate group linking the two bases. Regions of genomic sequences rich in the CpG pattern or "CpG islands" are resistant to methylation and tend to be associated with genes which are frequently switched on. It's been estimated that about half of all mammalian genes, and, possibly all mammalian house-keeping genes, have a CpG-rich region around their 5' end. Non-mammalian vertebrates have some CpG islands that are associated with genes, but the association gets equivocal in the farther taxonomic groups. The detection of CpG island upstream of predicted exons or genes is evidence in support of a highly expressed gene. As there is no official definition of what is a CpG island is or how to identify where they begin and end, we work with two definitions and thus two methods. These are: 1. cpgplot and newcpgreport use a sliding window within which the Observed/Expected ratio of CpG is calculated. For a sequence region to reported as a CpG island, it must satisfy the following contraints: Observed/Expected ratio > 0.6 % C + % G > 50% Sequence Length > 200 2. newcpgseek and cpgreport use a running sum calculated from all positions in a sequence rather than a window to produce a score. If there is not a CG dinucleotide at a position, the score is decremented, if there is one, the score is incremented by a constant (user-defined) value. If the score for a region in the sequence is higher than a threshold (17 at the moment) then a putative island is declared. Sequence regions scoring above the threshold are searched for recursively. This method 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. For most purposes you should probably use newcpgreport rather than cpgreport. It is 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. newcpgseek and cpgreport both now display the actual CpG count, the (%C + %G) and the Observed/Expected ratio in the region where the score is above the threshold. The geecee program measures CG content in the entire input sequence and is not to be used to detect CpG islands. It can be useful for detecting sequences that MIGHT contain an island. 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 Identify and plot CpG islands in nucleotide sequence(s) cpgreport Identify and report CpG-rich regions in nucleotide sequence(s) geecee Calculate fractional GC content of nucleic acid sequences newcpgreport Identify CpG islands in nucleotide sequence(s) Author(s) Rodrigo Lopez European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (1999) - Rodrigo Lopez Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None