Oxford Journals

Information for Authors

INSTRUCTION TO AUTHORS

AIMS AND SCOPE

DNA RESEARCH publishes research papers with original findings of substantial importance in broad aspects of DNA and genome-related research. Emphasis will be made on the following subjects: 1) Sequencing and characterization of genomes/important genomic regions, 2) Functional analysis of genes, gene families and genomes, 3) Techniques and equipments useful for structural and functional analysis of genes and genomes, 4) Comprehensive analysis of the structure and function of genes and genomes as well as relevant informatics methods and tools. (See 'Availability' section in SUBMISSION OF MANUSCRIPTS for specific instructions for manuscripts in this field.) Papers reporting sequence and mapping data will be considered for publication if the data are found to provide significant information in biology, or if the data are considered to be valuable for genome analysis. The journal also welcomes novel findings in other scientific disciplines related to genomes.

Information on the contents of DNA RESEARCH will be indexed in ISI® services, including Science Citation Index® and Current Contents®/Life Sciences.

OPEN ACCESS CHARGES

All articles published online in DNA RESEARCH have been, and will continue to be open to all readers without paid subscription. This has in the past been possible due to sponsorship by the Kazusa DNA Research Institute. However, it has been decided that sponsorship is no longer sufficient to ensure quality and to introduce new developments for the journal. The Editors of the journal value the importance of wide dissemination of information, and have made a difficult decision to introduce an Open Access charge to authors as a fee for publication in order to continue providing the online content without a subscription. The 2006 Open Access charge is $500.

The journal hopes that contributors to DNA Research will support the journal by paying the Open Access charge. However, under OUP’s existing Developing Countries Initiative, those based in List A and List B countries can apply for free online access to the Oxford Journals collection. More information about OUP’s Developing Countries Initiative can be found at http://www.oxfordjournals.org/jnls/devel/. The journal may also grant waivers when a manuscript is recommended by the Editorial Board as being of particularly high importance to the journal. Interested authors should contact the Editor in charge of review of their manuscript.

SUBMISSION OF MANUSCRIPTS

TYPE OF SUBMISSIONS

DNA RESEARCH publishes two types of paper: full papers and short communications.

Full Papers This type of paper is, in principle, limited to 8 printed pages (approximately 24 manuscript pages), but supporting data can be presented as supplementary data (for online-only publication), if accepted. The manuscript should be divided into the following sections: (1) title page, (2) abstract, (3) introduction, (4) materials and methods, (5) results and discussion, (6) references, (7) tables, and (8) figure legends. The title page, abstract, references, tables (each table), and figure legends must begin on a new page.

Covering letter: Prepare a covering letter briefly explaining your research and confirming that the required criteria for authorship mentioned in "Authorship" section are fulfilled.

Title page: The title page must contain a brief title which accurately describes the contents, and a running title of no more than 50 characters (including spaces). The names of all authors should be provided along with the full name and address of each institution. The name, complete address, and telephone and fax numbers should be provided for the author to whom correspondence should be addressed.

Abstract and key words: The abstract should be one paragraph of no more than 200 words summarizing the basic content of the paper. Avoid abbreviations and references. When it is essential to include a reference, a full literature citation except for the article title should be provided. After the abstract, between 3 and 5 key words should be included that will assist in cross indexing.

Introduction: State the reasons for performing the work with brief reference to relevant previous work (no longer than one type-written page).

Materials and Methods: Describe the materials and methods used to allow the experiments to be reproduced. Describe only the methods specifically used in detail. For commonly used methods, citation of references is sufficient.

Results and Discussion: This section can be divided into subsections with short subtitles. The conclusions are to be provided in this section.

Availability:
Papers on related informatics methods and tools (4. Comprehensive analysis of the structure and function of genes and genomes and/or related informatics methods and tools) should include a section on availability of the information on related software / database / URL addresses.

Acknowledgements: Include here the names of those to be acknowledged as well as all sources of financial support.

References: The references should be cited in the text in the order in which they first appear using superscript arabic numbers. List all authors when there are 6 or less; when 7 or more, list only the fist 3 authors followed by "et al." Abbreviations of journals must conform to those used in Index Medicus. The reference section should be arranged as follows:

Sprengel, R., Braun, T., Nikolics, K., Segaloff, D. L., and Seeburg, P. H. 1990, The testicular receptor for follicle cDNA stimulating hormone-Structure and functional expression of cloned cDNA, Mol. Endocrinol., 4, 525-530.
Sambrook, J., Frietsch, E. F., andManiatis, T. 1989, Molecular cloning: A LaboratoryManual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
Maxam, A. M. and Gilbert, W. 1980, In: Grossman, L.,Moldave, K. (eds)Methods in Enzymology, Vol. 65. Academic Press, New York, pp. 499-559.

Tables: Type each table on a separate page with a heading at the top and footnotes at the bottom. All acronyms and abbreviations must be defined.

Figures: All half-tone figures should be provided as high quality glossy photographic prints (although high-resolution electronic files will be required if your article is accepted). With light pencil, write the name of the first author and the figure number on the back of each figure. Figures will be reproduced either in a single (8.4 cm) or double (17 cm) column width. Half-tone and color figures should be provided in triplicate.

Figure legends: Figure legends should bear enough information to understand the figure without reference to the text.

Color photographs: Color photographs will be printed at an extra charge of £350 per page. Please indicate your willingness to pay the charge.

Supplementary data: Additional sequence or mapping data that provide supporting evidence to a paper can be published separately as online-only material. The materials to be included in this section should be provided in their final form and should include a brief description that provides enough information to the data. When references are included, a full citation should be provided. Please note that Supplementary data will not be edited, so ensure that it is clearly and succinctly presented, and that the style of terms conforms to the rest of the paper. Also ensure that the presentation will work on any internet browser.

Authorship: All persons designated as authors should qualify for authorship. The order of authorship should be a joint decision of the co-authors. Each author should have participated sufficiently in the work to take public responsibility for the content. Authorship credit should be based on substantial contribution to conception and design, execution, or analysis and interpretation of data. All authors should be involved in drafting the article or revising it critically for important intellectual content, and must have read and approved the final version of the manuscript. Assurance that all authors of the paper have fulfilled these criteria for authorship should be clearly stated in the covering letter.

Short Communications This type of paper must be no longer than 5 printed pages (approximately 15 manuscript pages), and should be divided into the following sections: (1) title page, (2) abstract, (3) text, (4) references, (5) tables, and (6) figure legends. The title page, abstract, references, tables (each table), and figure legends must begin on a new page. Start the text section with brief introduction to the work. Materials and methods should be included in the figure legends or table footnotes.

An additional category will newly be provided to publish Review articles on an invitation-basis. If you are interested in writing a review article on a topic of your expertise, please express your wish to any one of the editors in advance.

SUBMISSION ONLINE

DNA RESEARCH has launched an online submission system in April, 2006.

Follow the instructions above regarding the format of your manuscript and references.

Prepare your manuscript, including tables, using a word processing program and save it as a .doc, .rtf or .ps file. All files in these formats will be converted to .pdf format upon submission. Please note: This journal does not accept Microsoft Word 2007 documents at this time. Please use Word's "Save As" option to save your document as an older (.doc) file type. Prepare your figures at publication quality resolution, using applications capable of generating high-resolution .tif files (1200 d.p.i. for line drawings and 300 d.p.i. for colour and half-tone artwork). The printing process requires your figures to be in this format if your paper is accepted and printed. For useful information on preparing your figures for publication, go to http://cpc.cadmus.com/da.
Prepare any other files that are to be submitted for review, including any supplementary material. The permitted formats for these files are the same as for manuscripts and figures. Other file types, such as Microsoft Excel spreadsheets and Powerpoint presentations may be uploaded and will form part of the single .pdf file that is created for use in the peer review process. It is also possible to upload LaTeX files but these will not be automatically converted to .pdf format (and are therefore discouraged). The journal staff, editors and reviewers will only be able to view these unconverted files if they have the appropriate software, which cannot be guaranteed.
When naming your files, please use simple filenames and avoid special characters and spaces. If you are a Macintosh user, you must also type the three-letter extension at the end of the file name you choose (e.g. .doc, .rtf, .jpg, .gif, .tif, .ppt, .xls, .pdf, .eps, .mov).
The online submission software will automatically create a single .pdf file containing your main text and reduced-resolution versions of any figures you have submitted. This document will be used when your manuscript undergoes peer review. Your submitted files will appear in this .pdf sequentially, as specified by you on the submission page, and you will have an opportunity to enter figure captions/legends and to check the .pdf file prior to final submission. Please make sure that you proof the converted pdf file so no material is missing, and there are no conversion errors.

SUBMITTING YOUR MANUSCRIPT

Now that your files are ready, visit the online submission web site at http://mc.manuscriptcentral.com/dnar

First, you will need to log into the system. Note: Before you begin, you should be sure you are using an up to date version of Netscape or Internet Explorer. If you have an earlier version, you can download a free upgrade using the icons found at the bottom of the 'Instructions and Forms' section of the online submission web site.
- If you know your login details (i.e. you have submitted or reviewed a manuscript on this system before), use your User ID and Password to log on.
- If you do not know your login details, check to see if you are already registered by clicking on the 'Forgot your password' button and following the on-screen instructions. If you are not already registered, you can register by clicking on the 'Create account' button on the login screen and following the on-screen instructions.
- If you have trouble finding manuscripts or have other problems with your account do not create another account. Instead, please contact the journal's editorial office.
To submit a new manuscript, go to the 'Author Center', click on the blue star button which says ‘Click here to submit a new manuscript’ and then follow the on-screen instructions. There are up to 7 steps for you to follow to submit your manuscript. You move from one step to the next by clicking on the 'Next' button on each screen or back to the previous screen by clicking on the 'Previous' button. Please note that if you click on the 'Back' or 'Forward' button on your browser, the information you have entered will not be saved. At any stage you can stop the submission process by clicking on the 'Main Menu' or the ‘Author Dashboard’link. Everything you have typed into the system will be saved. , and the partially completed submission will appear under 'unsubmitted manuscripts' in your 'Author Center'. To return to the submission process you will need to click on the button 'Continue Submission' against the relevant manuscript title.
When submitting your manuscript, please enter your manuscript data into the relevant fields, following the detailed instructions given at the top of each page. You may like to have the original word processing file available so that you can copy and paste the title and abstract into the required fields. You will also be required to provide email addresses for your co-authors, so please have these to hand when you logon to the site.
When you come to upload your manuscript files via the 'File Upload' screen:
- Enter individual files using the 'Browse' buttons below and select the appropriate 'File content' type.
- Select the document's designation from the pull-down menu.
- Upload your files by clicking on the 'Upload files' button. This converts your files to a PDF and may take several minutes. Repeat these steps until you have uploaded all your files.
- When the upload of each file is completed, you will see a confirmation window and will be prompted to provide figure legends and 'file tags' that will link figures to texts in the HTML proof of your main document.
- Once you have uploaded all files, indicate the order in which they should appear in your paper. This will determine the order in which they appear in the consolidated PDF used for peer review.
- After the successful upload of your text and images, you will need to view and proof your manuscript. Please do this by clicking on the blue HTML button or a PDF button.
- If the files have not been uploaded to your satisfaction, go back to the file upload screen where you can remove the files you do not want, and repeat the upload process.
When you are satisfied with the uploaded manuscript proof click on 'Next' which will take you to the 'Review & Submit' screen. The system will check that you have completed all the mandatory fields and that you have viewed your manuscript proof. It will also present you with a summary of all the information you have provided and give you a final chance to edit it. When you have finished reviewing this information press 'Submit'.
After the manuscript has been submitted you will see a confirmation screen and receive an email confirmation stating that your manuscript has been successfully submitted. This will also give the assigned manuscript number, which is used in all correspondence. If you do not receive this, your manuscript will not have been successfully submitted to the journal and the paper cannot progress to peer review. If this is the case your manuscript will still be sitting in the 'Unsubmitted Manuscripts' section of your 'Author Center' awaiting your attention.
If you return to your 'Author Center' you will notice that your newly submitted manuscript can be found in the 'Submitted Manuscripts' area. Among the information listed there, the 'Processing Status' section provides information on the status of your manuscript as it moves through the review process.

SUBMITTING A REVISED MANUSCRIPT

Logon to the online submission web site as before and, in the 'Author Center', click on 'Manuscripts with Decisions'. You will then see the title of any manuscripts you submitted that have decisions. If the decision requires submission of a revised paper, click on “create a revision.” You will reach the revision submission procedure.
First, you will be asked to respond to the decision letter for the original submission. The next steps will be the same as the original submission procedure. When you reach the File Upload stage, you will see that the files from the original submission will already be uploaded for you. Please delete any files that you revised, and upload the new files.
If you need to logout during the submission procedure and need to continue the process, go to the ‘Author Center’ and click on ‘Revised Manuscripts in Draft.’ Click on the blue ‘Continue Submission’ button, and you may resume submission.

IMPORTANT. As detailed above, your images are required as high-resolution .tif files (1200 d.p.i. for line drawings and 300 d.p.i. for colour and half-tone artwork). If this is not possible, high quality print outs on glossy paper can be used. For useful information on preparing your figures for publication, go to http://cpc.cadmus.com/da. Please note that publication of your manuscript will not proceed until figures suitable for reproduction are received.

GETTING HELP

If you experience any problems during the online submission process please consult the Author's User Guide, which provides more detailed submission instructions, and 'movie tutorials' explaining how to submit your paper. Alternatively, please contact the journal's editorial office who will be pleased to assist you.

SPEED OF PUBLICATION

DNA RESEARCH will make every attempt to publish papers within 3 to 4 months after their receipt. However, when the manuscript must undergo extensive English editing, it may result in a delay.

REVIEW PROCESS

All manuscripts are reviewed by members of the editorial board or by qualified reviewers. Authors are notified, generally within 6 weeks after submission, of the editors' decision. When a manuscript is returned to the author for modification, it should be returned to the editor within 3 months: otherwise it may be considered withdrawn.

PAGE PROOFS

Page proofs are sent to authors by email. Proofs should be checked immediately for typographical errors and returned to the publishers by email or facsimile. Excessive alterations may delay publication of the paper.

PAGE CHARGES

No page charges are levied. However, authors may be charged for extensive English editing or excessive changes made at the page proof stage.

OFFPRINTS

An offprint purchase order form will be sent to the authors with each proof.

NUCLEOTIDE SEQUENCES

GenBank, EMBL or DDBJ accession numbers for nucleotide and/or amino acid sequence data must be included in the manuscript.

PRESENTATION OF SEQUENCE DATA

Nucleotide sequences may be presented in the following format. The sequence should be submitted as cameraready copy in the dimension of 17 cm (width) x24 cm (height). Use a laser-quality computer printer, and print the sequence single or double-spaced in lines of 120 to 150 nucleotides. The sequence is recommended to be further subdivided into blocks of 10 or 20 nucleotides by inserting spaces or by marking every 10 or 20 nucleotides. Number each sequence line in the left margin by indicating the first base of each line. In order to designate exons and introns, coding regions, transcribed regions etc., uppercase and lowercase letters may be used. Encoded amino acid sequences may be presented, using single-letter amino acid codes.