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Updated September 1999
Please read these guidelines carefully and follow them strictly to ensure that the review and publication of your paper is as efficient as possible.
Nucleic Acids Research (NAR) provides rapid publication for papers on physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions.
Survey and Summaries
This section provides a format for brief reviews. The section heading is deliberately chosen so that material not normally acceptable in a formal review article can be presented.
Standard papers
Papers are included under the following categories: RNA, Molecular Biology, Chemistry, Genomics, Computational Biology and Structural Biology.
Methods
Significant new methods can be published in two forms.
Database issue
The first issue of each year is a special one devoted to biological databases. Authors proposing to submit an article describing a new database, not previously featured, are encouraged to contact Dr R. J. Roberts (Tel: +1 978 927 3382; Fax: +1 978 921 1527; Email: roberts{at}neb.com) before July 1, 2000.
Materials
It is our continued policy that all strains, clones, cell lines, hybridomas, X-ray and NMR coordinates, and computer programs that are described in publications in the Journal should be made immediately available to any qualified investigator upon request. Authors submitting manuscripts to NAR must agree to adhere to this policy. The Editors are prepared to deny further publication rights in the Journal to authors unwilling to abide by this principle.
Author's responsibilities
Submission of a manuscript implies that it reports unpublished work and that it is not under consideration elsewhere. The signature of the corresponding author is on behalf of all authors and assumes that they are in complete agreement with the contents of the manuscript and are prepared to abide by the policies of the Journal.
Copyright and authorisations
If previously published tables, illustrations or more than 200 words of text are to be included, then the copyright holder's permission must be obtained, and copies of any such permission letters should be enclosed with the manuscript. Authors must obtain authorisation for all personal communications. Appropriate letters should accompany manuscripts.
Joint first authorship
A footnote will be allowed provided that the original submission is accompanied by a separate letter, signed by all authors, containing the statement: `The authors wish it to be known that, in their opinion, the first x authors should be regarded as joint First Authors'. Other statements concerning joint authorship will not be published.
NAR OnlineAll manuscripts accepted for publication will be posted electronically on the NAR web site. Papers may appear up to two weeks before the cover date of the bound copy. For author-downloading of PDF files, see OFFPRINTS.
Other considerations
The Editors will honour requests for back-to-back publication only if the manuscripts are submitted together, to the same editorial office, with a joint signed undertaking indicating consent.
Nucleic acid sequence data
All sequence information must be submitted in electronic form to any of the three major collaborative databases (EMBL/GenBank/DDBJ) for an accession number. It is necessary to submit sequences to one database only since data are exchanged between EMBL, GenBank and DDBJ on a daily basis.
New sequence names and their accession numbers should be listed at the beginning of the Materials and Methods section to aid reader searches.
Contact information for EMBL:
EMBL Nucleotide Sequence Submissions
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Tel: +44 (0)1223 494411; Fax: +44 (0)1223 494472
Email: DATASUBS{at}EBI.AC.UK
http://www.ebi.ac.uk/
Contact information for GenBank:
National Center for Biotechnology Information
National Library of Medicine
Building 38A, Room 8N-803
Bethesda, MD 20894, USA
Tel: +1 301 496 2475; Fax: +1 301 480 9241
Email: gb-sub{at}ncbi.nlm.nih.gov
http://www.ncbi.nlm.nih.gov/
Contact information for DDBJ:
DNA Data Bank of Japan
Center for Information Biology
National Institute of Genetics
Mishima, Shizuoka 411, Japan
Tel: +81 559 81 6853; Fax: +81 559 81 8849
Email: ddbjsub{at}ddbj.nig.ac.jp (for data submissions)
http://www.ddbj.nig.ac.jp/
Protein sequence data
All protein sequence data should be deposited with:
Protein Identification Resource
National Biomedical Research Foundation
Georgetown University Medical Center
Washington, DC 20007, USA
Tel: +1 202 687 2121; Fax: +1 202 687 1662
Molecular models
Atomic co-ordinates used to create molecular models described in a manuscript, not readily available elsewhere, must be made available as supplementary material through the online version of NAR.
Crystal and NMR structures
Atomic co-ordinates and structure factor amplitudes should be deposited with a database, without a delayed release date, simultaneously with manuscript submission. The appropriate databases are listed as follows.
Cambridge Crystallographic Data Centre (CCDC). For deposition of data on nucleosides, nucleotides and other small molecules.
Contact information:
CCDC
12 Union Road
Cambridge CB2 1EZ, UK
Tel: +44 (0)1223 336408; Fax: +44 (0)1223 336033
Email: fileserv{at}chemcrys.cam.ac.uk containing the single line text "sendme depform"
http://www.ccdc.cam.ac.uk
Protein Data Bank (PDB). For deposition of atomic coordinate and structure factor data for proteins determined by X-ray and for all macromolecules determined by NMR methods with the PDB at Brookhaven National Laboratories.
Contact information:
Protein Data Bank
Department of Chemistry,
Rutgers University,
610 Taylor Road,
Piscataway,
NJ 08854-8087, USA
Tel: +1 732 445 0103
Fax: +1 732 445 4320
http://www.rcsb.org/pdb/
or with the PDB at the European Bioinformatics Institute:
http://www2.ebi.ac.uk/pdb
Nucleic Acid Database (NDB). Atomic coordinate and structure factor data for crystal structures of nucleic acids should be deposited directly with the NDB. Once the data are processed they will be forwarded to the PDB for deposit in the single central archive. All crystal structure data for DNA and RNA will continue to be available from both the NDB and PDB.
Coordinates, structure factors and a current NDB deposition form should be emailed and a hard copy of the related manuscript should be mailed or faxed to the postal address.
Contact information:
The Nucleic Acids Database
Department of Chemistry
Rutgers, The State University of New Jersey
610 Taylor Road, Piscataway
NJ 08854-8087, USA
Fax: +1 732 445 4320
Email: ndbadmin{at}ndbserver.rutgers.edu
http://ndbserver.rutgers.edu/
Deposition numbers for PDB and NDB must be sent to the Editor dealing with the manuscript as soon as received. Manuscripts will not be published until the Journal is in receipt of a PDB/NDB number.
Length
Papers should be of a length appropriate for the amount of information contained but should not usually exceed 8 printed pages except where further reduction would eliminate critical information. Exceptions might include Structural Biology, Genomics and Survey and Summaries. The relevant calculation is on the manuscript submittal form. All text should be double spaced and pages should be numbered.
Abstract
The abstract should be a single paragraph, not exceeding 200 words. No references should be cited.
References
These should be cited in the text by sequential number only, in order of appearance, and listed numerically in the References section. Authors should check carefully that all references in the References section are cited in the text. Multi-references under one number are not allowed since this format is not recognised by the Medline linking system in NAR Online. Personal communications, unpublished results, manuscripts submitted or in preparation and Internet/web sites should be cited in the text only, NOT included in the References section. Two copies of unpublished manuscripts should be supplied for the referees.
The citation of journals (abbreviated in the style of Chemical Abstracts), books and multi-author books and sequence data not published and only available from the databank entry should conform with the following examples:
1. Schmitt,E., Panvert,M., Blanquet,S. and Mechulam,Y. (1995) Nucleic Acids Res., 23, 4793-4798.
2. Huynh,T.V., Young,R.A. and Davies,R.W. (1988) In Glover,D.M. (ed.), DNA Cloning-A Practical Approach. IRL Press, Oxford, Vol. I, pp. 49-78.
3. Maniatis,T., Fritsch,E.F. and Sambrook,J. (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
4. Burnett,R.C. (1993) EMBL accession no. X52486.
5. Smith,A.B. (1999) Nucleic Acids Res., 27, e1.
References of the type Smith et al. (1989) must not be used. However, where the list of authors is extensive it is acceptable to list the first 10 authors followed by et al.
In Survey and Summary articles, full titles may be included in the References at the Executive Editor's discretion.
Authors are encouraged to cite accession numbers wherever possible either within the text or in the form of a reference, as per example 4 above.
Figures
Hard copy submission. Hard copies of figures should always be provided. Each figure should be referred to in the text and marked on the back with the number and the name of the first author. The area of a page available for figures is 230 mm (height); 178 mm (width) and figures should not exceed these dimensions. A single column is 84 mm wide and a double column is 178 mm wide. Ideally a figure should fit either a single or double column. Any lettering should be approximately 2 mm in height and should be of a consistent size within each figure. If submitting figures that require reduction, please ensure that the lettering will be clearly legible after reduction to final size. Photographs should be provided as high quality glossy prints in order to withstand the inevitable loss of contrast and detail inherent in the printing process. Line drawings should be provided as good quality hard copies suitable for reproduction as submitted. Shading used on line drawings should be clear and distinctive; shades of grey will not reproduce and small patches of white on an otherwise black background are likely to be lost on reproduction.
Electronic submission. Electronic images may be supplied in addition to, but not as substitutes for, hard copies. Figures should be supplied in separate files, NOT embedded within the text, preferably on a separate disk to the text. Minimum acceptable resolutions for printing are 300 d.p.i. for colour or tone images; 1200 d.p.i. for line drawings. Preferred formats are TIFF, JPEG, PDF, EPS, BMP, Photoshop. Acceptable formats are MacPaint, PCX, PICT files, PIXNAR, PixelPaint, PHG, Scitex CT, Targa, Aldus Filemaker, Illustrator, and compression programs, e.g. .bin, .zip. The following formats are NOT suitable: Canvas 5, ClarisDraw, PostScript, PageMaker, CorelDraw, Microsoft Publisher, Adobe in Design.
Colour figures. The use of colour figures is encouraged where it improves clarity, and printing is free of charge. (Note, however, that printed offprints of papers containing colour figures are subject to a 110% surcharge.) Coloured schematics are preferred for comparative sequence data. If the data shown are computer-generated images (such as those from a phosphoimager) the relationship between the signal and the image intensity over a specified range must be stated (e.g. linear or sigmoidal). Unless it is stated to the contrary, it is assumed that all except background signals will be within this range and that the image will be unedited.
Figure legends. All figure legends should be included on the disk at the end of the text file. Symbols must NOT be included in figure legends; ALL symbols used in figures should be described in the legend using words.
Cover figures
Authors submitting figures which may be suitable for use on the cover of Nucleic Acids Research are encouraged to contact an Executive Editor. Such figures must be related to the manuscript they accompany, but must not be the same as a figure or part of a figure within the manuscript itself; i.e. an extra, different colour figure is required. Figures should be created on a dark colour block background and supplied as clean, hard copy on photographic paper. An electronic copy of the figure can be supplied as a TIFF file (in addition to hard copy) at a minimum resolution of 300 d.p.i. and, ideally, saved with the CMYK colour option, and of a size that will require no reduction or enlargement before reproduction (width 216 mm; depth 179 mm; inclusive of background). Colours should be bright and clearly distinct from one another. The author will be supplied with proofs of the cover for approval prior to printing and a gratis copy of the issue on which the cover appears.
Supplementary material
Only directly relevant experimental data should be included in the full text of manuscripts. Supporting data should be submitted for review as supplementary material alongside the original manuscript for publication online only. Material which has not been peer-reviewed will be made available only through a link to the author's home page, at the discretion of the Editor. Papers containing online supplementary material will be designated `S` on the contents page.
Computational Biology papers
Authors should include two copies of an executable version of the program and instructions for use by the referees. Any costs associated with a reader acquiring the program must be specified in the text.
NMR papers
Resonance assignments should be reported relative to DSS and not to HOD.
Disk preparation
Whilst we can accept most computer and word processor disks, the preferred combinations are PC Windows, MS-DOS or Apple Mac with either Word or Wordperfect. If you are using a new version of the software, before you submit your disk, you must also save the file in RTF.
Figure captions and tables should be inserted at the end of the manuscript file.
Do not enter carriage returns to obtain spacing between lines, paragraphs, references, etc. since the space required is generated automatically by the typesetters. Do not use double spaces after each sentence within a paragraph. Do not use the endnote, running titles and footnote features of your word processing programme. Do not include any copyright material (e.g. word processor software or operating system files) on the disk.
It is important that the final copy of your manuscript is checked carefully because spelling mistakes, inconsistencies and errors will be faithfully translated into the typeset copy. In the case of a mismatch between disk and hard copy, the hard copy will be taken as the definitive version.
After the manuscript has gone through all the review and editing stages, copy the data to a clean, newly formatted disk. Do not copy any irrelevant files and/or back-up files onto the disk.
Apple Mac users should ensure that the disk wastebasket is empty before submitting the disk.
Clearly mark the manuscript number, file name and first author's name on the disk.
Please note that Oxford University Press will not return the disk.
LaTeX
Authors should note that LaTeX is a typesetting program and therefore not compatible with our editorial and typesetting systems. Authors able to supply only LaTeX are requested to ensure that all macros are inserted at the head of the file, and that references and figure legends are embedded rather than linked to external files.
Proofs of the edited text will be faxed to the corresponding author for the correction of typographical errors only and should be returned, by fax, within 24 hours. Any other substantial changes and notes added in proof will necessitate Editorial approval. Corrections should be marked on the proof and listed separately for clarification. It is the responsibility of the corresponding author to ensure that all co-authors agree with any corrections made. Please note that authors will not normally receive figure proofs, and should therefore ensure at submission and after revision that all figures and figure legends are accurate and in agreement.
It is a condition of publication in Nucleic Acids Research that authors assign copyright to Oxford University Press. This ensures that requests from third parties to reproduce articles are handled efficiently and consistently and will also allow the article to be as widely disseminated as possible. In assigning copyright, authors may use their own material in other publications provided that Nucleic Acids Research is acknowledged as the original place of publication, and Oxford University Press is notified in writing in advance. A (13 kb PDF file) must be completed and returned at the time of revision.
For standard papers, the publishers either supply 30 free offprints or give permission for one author to download the PDF file of their article and place it on their own web site free of charge. Additional offprints are available for a charge. Offprints of papers containing colour figures are subject to a 110% surcharge. An offprint order form (19 kb PDF file) detailing these options should be completed and returned directly to the publisher on acceptance. (Authors should note that online figures are at a lower resolution than those in the printed copy: figures in offprints printed from PDF files will therefore be at lower resolution than those in offprints produced at the time of printing.)
For online-only papers, the publishers will give permission for one author to download the PDF file of their article and mount it on their web site. Note that printed offprints are not available and an offprint order form should not be returned for these papers.
For further information contact:
Nucleic Acids Research
Journals Department
Oxford University Press
Great Clarendon Street
Oxford OX2 6DP, UK
Tel: +44 (0)1865 556767; Fax: +44 (0)1865 267829
Email: jnl.nar{at}oup.co.uk
Three hard copies of the manuscript and three sets of figures should be submitted, accompanied by a completed manuscript submittal form. An electronic version should NOT be included with the initial submission. A covering letter should be included explaining why rapid publication in the Journal is appropriate and outlining any special considerations with respect to Editorial policy.
To expedite the review process, authors are requested to notify the submission office (by email) of details of manuscripts sent, including title, authors and abstract.
Authors are requested to recommend (and supply relevant contact details for) six qualified reviewers. These individuals should not have collaborated with the authors in the last few years. The refereeing process is usually more timely if the referees suggested are predominantly from within the geographical area covered by the editorial office to which the manuscript is submitted.
Authors should supply a list of five keywords as an aid to manuscript processing.
Revised manuscripts should be returned to the assigned editorial office within 60 days. Manuscripts returned late will be given a new submission (resubmission) date. [For those returned after 60 days but before 90 days (i.e. less than 30 days late), the resubmission date will become that date by which the revised manuscript should have been received in the editorial office. For those manuscripts returned after 90 days (i.e. more that 30 days late), the resubmission date will become the actual date of receipt of the revised manuscript in the editorial office.] An electronic version of the full
All Computational Biology, all Survey and Summaries
The Editor, Nucleic Acids Research
New England Biolabs, 32 Tozer Road
Beverly, MA 01915, USA
Tel: +1 978 927 3382; Fax: +1 978 921 1527
Email: otto{at}neb.com
Methods from the Americas, Japan, China and Korea
The Editor, Nucleic Acids Research
New England Biolabs, 32 Tozer Road
Beverly, MA 01915, USA
Tel: +1 978 927 3382; Fax: +1 978 921 1527
Email: otto{at}neb.com
Methods from the Rest of the World
Dr. Keith R. Fox, Nucleic Acids Research,
Division of Biochemistry & Molecular Biology,
School of Biological Sciences, University of Southampton,
Bassett Crescent East, Southampton SO16 7PX, UK
Tel: 44 2380 594 374; Fax: 44 2380 597 748
Email: foxnar{at}soton.ac.uk
Other Categories from the Americas
The Editor, Nucleic Acids Research
New England Biolabs, 32 Tozer Road
Beverly, MA 01915, USA
Tel: +1 978 927 3382; Fax: +1 978 921 1527
Email: otto{at}neb.com
Other Categories from the Rest of the World including Japan, China and Korea
Dr M. J. Gait, Nucleic Acids Research
Medical Research Council
Laboratory of Molecular Biology, Hills Road
Cambridge CB2 2QH, UK
Tel: +44 (0)1223 248011 or +44 (0)1223 402474;
Fax: +44 (0)1223 402070
Email: nar{at}mrc-lmb.cam.ac.uk
Please note: if a customs declaration is required, it is essential that the contents are listed as OF NO COMMERCIAL VALUE. Bills for Customs or VAT will be returned to the author.
The Journal can publish only a fraction of the manuscripts it receives. For this reason, the Editors insist that all manuscripts considered for publication must present some novel development and meet the criteria of originality, timeliness, significance and scientific excellence.
Sequences
Only those manuscripts will be considered in which new sequences are accompanied by complementary data with relevance to genomic organisation, transcription, RNA processing, expression, genetic analysis or other novel biology; the reported sequence must shed significant new light on basic questions of structural or functional interest. Manuscripts describing gene cloning or comparative sequence analysis will be considered only if the genes are of relevance to nucleic acid metabolism or interactions and some new important findings emerge. Sequences of genes for well-studied RNAs (as well as the RNA sequences themselves) are not acceptable unless of unusual interest. Nucleic acid sequences must be deposited in the databank; only those parts relevant to the discussion of the results will be printed.
Computational biology
Manuscripts will be considered if they describe novel applications or algorithms relevant to nucleic acid or protein sequence manipulation. Small improvements in existing programs or variations of well-established algorithms will generally not be suitable. Manuscripts describing the computational analysis of DNA or protein sequences (data mining) will be considered if they lead to biologically interesting conclusions that have been tested experimentally where possible.
Promoters
Manuscripts describing promoters or other regulatory elements will be considered only if they reveal significant new insights into regulatory mechanisms. Such manuscripts may include those that define:
The Journal also encourages manuscripts that report:
The Journal discourages manuscripts that report:
Manuscripts presenting construction of vectors or clone banks, the preparation of monoclonal antibodies or the isolation of nucleic acids will not be considered unless they are based on completely new principles or accompanied by novel biological applications.
Restriction enzymes and methylases
Manuscripts describing the identification of restriction enzymes or methylases with novel recognition sequences will be considered for publication in NAR Methods Online.
Oligonucleotide synthesis, antisense and ribozymes
The Journal encourages manuscripts describing:
The Journal discourages manuscripts describing:
Small molecule-nucleic acid interactions
Manuscripts will be considered only if they present substantial new information relevant to nucleic acid structure.
Genomics
Manuscripts should include complete chromosomal or genomic sequences and their comparative analysis or should describe new insights into biological problems through whole genomic approaches e.g. proteomics, analysis of EST or SAGE libraries or the use of array technologies.
Chromosome assignment
Manuscripts that present only cytological data are not acceptable.
NMR
Manuscripts containing a simple NMR assignment are not acceptable. Only those that present new structural information not previously available from other methods will be considered.
Differential splicing
Manuscripts that merely describe intron/exon locations for differentially spliced transcripts will usually not be considered, unless they include fully documented novel sequences at junctions or highly unusual arrangements of sequences that would suggest unexpected biological properties. The Journal encourages manuscripts describing:
New biological insights suggested by the sequences must be accompanied by experimental evidence.
Repetitive DNA
The Journal encourages manuscripts that describe novel insights into the regulated expression and function of SINEs, LINEs and other repetitive sequences. The Journal discourages manuscripts that describe the identification of new subfamilies or refinement of existing subfamilies, the relative mobilities of such subfamilies, or evolutionary studies and sequence comparisons, unless they provide novel insights.
In vitro nucleic acid selection
Manuscripts based on in vitro selection of RNA or DNA from random pools should include substantial new information relevant to nucleic acid structure and function, or to proteins that interact with nucleic acids. Manuscripts dealing solely with the isolation of an affinity ligand for a protein not involved in nucleic acid metabolism or interactions will normally not be considered. Manuscripts dealing with improvements in nucleic acid selection methodology will be considered under current methods guidelines i.e. only those manuscripts reporting developments of the highest originality and usefulness will be published in NAR Methods Online.
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