OJVR Referee Forms

REVIEWERS SUMMARY

In silico identification of tandem inter/intra-generic genetic elements (TIGE) using a random nucleotide generating Perl program:
A potential approach for locating structure-function regions of recently sequenced genomes

            This work describes a simple Perl program to match a gene sequence with specific function. Authors found tandem sequences (TIGE) using the criteria "query sequences whose
            adjoining 20 + nucleotide blocks showed at least near-contiguous identity with another non-duplicate database sequence" The authors go on to speculate that TIGE represent short
            DNA sequences which could be "hallmarks of evolution" Examples of TIGE showing 100% identity with known regions of human and animal chromosomes are provide to support their
            conclusions. This works adds to the plethora of algorithms generated to link gene sequence to function. The advantage of the present being its simplicity and capacity to be processed
            by a large number of investigators with low cost (as mentioned by authors) .

Detailed editorial comments below:

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REFEREE FORM

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Author(s): Prokash K and Stashenko P
ID Number: (QW29510)
Title: In silico identification of tandem inter/intra-generic genetic elements (TIGE) using a random nucleotide generating Perl program: A potential approach for locating structure-function regions of recently sequenced genomes

The Editorial board must ensure that the OJB publishes only papers which are scientifically sound. To achieve this objective, the referees are requested to assist the Editors by making an assessment of a paper submitted for publication by:

(a) Writing a report as described in GENERAL STATEMENTS (Below),
(b} Check the boxes shown below under 1. and 2. ( YES or NO) [N.B.A "NO" assessment must be supported by specific comment in the report.
(c) Make a recommendation under 3.

The Editor-in-Chief would appreciate hearing from any referee who feels that he/she will be unable to review a manuscript within four weeks.

1. CRITERIA FOR JUDGEMENT (Mark "Yes" or "No").

General statements

What is this work about? (please describe) This work describes a simple Perl program to match a gene sequence with specific function. Authors found tandem sequences (TIGE)

            using the criteria "query sequences whose adjoining 20 + nucleotide blocks showed at least near-contiguous identity with another non-duplicate database sequence" The authors go
            on to speculate that TIGE represent short DNA sequences which could be "hallmarks of evolution" Examples of TIGE showing 100% identity with known regions of human and animal
            chromosomes are provide to support their conclusions.

Does it add any value to current knowledge (in this area of bioinformatics)? It could add-to/improve algorithms currently available to link gene sequence to function and speed up
the process

Is it innovative? Yes in the sense mainly that it provides another tool which would be freely available

Yes/No answers.

Is the work scientifically sound?Y

Is the work an original contribution Y
Are the conclusions justified on the evidence presented? Y
Is the work free of major errors in fact, logic or technique? Y
Is the paper clearly and concisely written? Y
Do you consider that the data provided on the care and use of animals (See Instructions to Contributors) is sufficient to establish that the animals used in the experiments were well looked after, that care was taken to avoid distress, and that there was no unethical use of animals? NR

2 PRESENTATION (Mark "Yes" or "No").

Does the title clearly indicate the content of the paper? Y
Does the abstract convey the essence of the article? Y
Are all the tables essential? Y
Are the figures and drawings of good quality? Y
Are the illustrations necessary for an understanding of the text? Y
Is the labelling adequate?Y

3. RECOMMENDATIONS(Mark one with an X)

Not suitable for publication in the OJB
Reassess after major changes
Reassess after suggested changes
Accept for publication with minor changes X
Accept for publication without changes

4. REPORT (here you place your detailed comments) This works adds to the plethora of algorithms generated to link gene sequence to function. The advantage of the present being its simplicity and capacity to be processed by a large number of investigators with low cost (as mentioned by authors) . There is the question of whether the criteria used for TIGE is 100% valid and also that the similarities to the random query sequences occurred just by chance (although highly unlikely). ABSTRACT: would prefer to change "likely" to "may" represent ...hallmark of evolution. INTRODUCTION : remove "very" from difficult to relate ect...Please clarify the meaning the last sentence in paragraph 1 ie "above identification process" ect...METHODS: A small explanation of "vector contamination" would be helpful here. RESULTS: NC/. Publish with minor changes.

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