When appropriate, material such as sequence alignments and large tables can be published online as supplementary material permanently linked to an article in the online journal. The majority of the information in Protocols will be published in Supplementary Material with the main text as the major section, with subsections allowed.
The Supplementary Material section should only list any supplementary material available online at the MBE website. All material to be considered as supplementary data must be submitted at the same time as the main manuscript for peer review.
A maximum of 5 files are acceptable to make up the supplementary material unit for an article. The maximum size per file should not exceed 2 MB (though text files should be a great deal smaller), and files must be as small as possible, so that they can be downloaded quickly. An HTML index page is usually created to link the supplementary data file(s) to the article. Provide short (2-4 word) titles for each individual file; these will be used to create links to the files from the index page.
Files submitted as supplementary material must be correct and complete, including figure legends, etc. These files will not be edited or reformatted, but are posted exactly as submitted.
The following formats are acceptable: Plain text (.txt); HTML (.html, htm); Jpeg (.jpg, .jpeg); GIF (.gif); QuickTime video (.mov); MPEG Movie (.mpg); Microsoft AVI Video (.avi); Adobe PDF (.pdf); Microsoft Excel Spreadsheet (.xls); Microsoft Word (.docx)
Sequence alignments should be submitted as supplementary material in two forms:
- As a text file in a "sequential" format such as fasta, so that readers can download and use the alignment, or
- In an "aligned" or "interleaved" format, so that readers can easily view the alignment.
Links from articles to online supplementary material will be inserted as soon as articles are published online (approximately one week after acceptance).
Among the requirements for publication in MBE is that authors make publicly available, free of charge, any alignment data, strains, cell lines, or clones used in reported experiments, computer code essential to the analysis, and any other material or information necessary for the assessment and verification of findings or interpretations presented in the publication. Substantial computer software essential to the publication that has not previously been published must be provided as Supplementary Material or made available through a publicly accessible repository.
Newly reported sequences must be deposited in the DDBJ/EMBL/GenBank database (see below). Accession numbers must be included in the final version of the manuscript and cannot be added at the proof stage.
Nucleotide sequences must be accurate. Measures employed to avoid error should be clearly stated. Determining the sequence on both strands is the standard for most studies. When only one strand is sequenced, this must be explicitly stated both in Materials and Methods and in the entry that is submitted to one of the sequence databases.
All ambiguous positions in a nucleotide sequence must be indicated with the appropriate IUBMB single-letter code (see "Terminology" in General Author Guidelines), rather than "resolved" by guesswork.
Newly reported nucleic acid and amino acid sequences, microarray data, structural coordinates, and all other essential information must be submitted to appropriate public databases (e.g., GenBank; the EMBL Nucleotide Sequence Database; DNA Database of Japan; the Protein Data Bank; Swiss-Prot; GEO; and Array-Express). Methods must be described in sufficient detail to permit independent replication. Standard procedures can be referenced, provided that significant variations are adequately described. Evaluation of large-scale experiments such as transcript profiling using microarray- or deep sequencing-based approaches requires a complete and transparent description of each experiment, of the nature of the replication, and of the statistical analysis, including, for example, whether any multiple comparison correction was applied. Large-scale data sets necessary for peer review must be made available to reviewers at the time of submission.
Sequence alignments can also be deposited at EMBL-ALIGN.
Updated on 15th October 2012
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