Journal of Clinical and Diagnostic Research, ISSN - 0973 - 709X

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Dr Bhanu K Bhakhri

"The Journal of Clinical and Diagnostic Research (JCDR) has been in operation since almost a decade. It has contributed a huge number of peer reviewed articles, across a spectrum of medical disciplines, to the medical literature.
Its wide based indexing and open access publications attracts many authors as well as readers
For authors, the manuscripts can be uploaded online through an easily navigable portal, on other hand, reviewers appreciate the systematic handling of all manuscripts. The way JCDR has emerged as an effective medium for publishing wide array of observations in Indian context, I wish the editorial team success in their endeavour"

Dr Bhanu K Bhakhri
Faculty, Pediatric Medicine
Super Speciality Paediatric Hospital and Post Graduate Teaching Institute, Noida
On Sep 2018

Dr Mohan Z Mani

"Thank you very much for having published my article in record time.I would like to compliment you and your entire staff for your promptness, courtesy, and willingness to be customer friendly, which is quite unusual.I was given your reference by a colleague in pathology,and was able to directly phone your editorial office for clarifications.I would particularly like to thank the publication managers and the Assistant Editor who were following up my article. I would also like to thank you for adjusting the money I paid initially into payment for my modified article,and refunding the balance.
I wish all success to your journal and look forward to sending you any suitable similar article in future"

Dr Mohan Z Mani,
Professor & Head,
Department of Dematolgy,
Believers Church Medical College,
Thiruvalla, Kerala
On Sep 2018

Prof. Somashekhar Nimbalkar

"Over the last few years, we have published our research regularly in Journal of Clinical and Diagnostic Research. Having published in more than 20 high impact journals over the last five years including several high impact ones and reviewing articles for even more journals across my fields of interest, we value our published work in JCDR for their high standards in publishing scientific articles. The ease of submission, the rapid reviews in under a month, the high quality of their reviewers and keen attention to the final process of proofs and publication, ensure that there are no mistakes in the final article. We have been asked clarifications on several occasions and have been happy to provide them and it exemplifies the commitment to quality of the team at JCDR."

Prof. Somashekhar Nimbalkar
Head, Department of Pediatrics, Pramukhswami Medical College, Karamsad
Chairman, Research Group, Charutar Arogya Mandal, Karamsad
National Joint Coordinator - Advanced IAP NNF NRP Program
Ex-Member, Governing Body, National Neonatology Forum, New Delhi
Ex-President - National Neonatology Forum Gujarat State Chapter
Department of Pediatrics, Pramukhswami Medical College, Karamsad, Anand, Gujarat.
On Sep 2018

Dr. Kalyani R

"Journal of Clinical and Diagnostic Research is at present a well-known Indian originated scientific journal which started with a humble beginning. I have been associated with this journal since many years. I appreciate the Editor, Dr. Hemant Jain, for his constant effort in bringing up this journal to the present status right from the scratch. The journal is multidisciplinary. It encourages in publishing the scientific articles from postgraduates and also the beginners who start their career. At the same time the journal also caters for the high quality articles from specialty and super-specialty researchers. Hence it provides a platform for the scientist and researchers to publish. The other aspect of it is, the readers get the information regarding the most recent developments in science which can be used for teaching, research, treating patients and to some extent take preventive measures against certain diseases. The journal is contributing immensely to the society at national and international level."

Dr Kalyani R
Professor and Head
Department of Pathology
Sri Devaraj Urs Medical College
Sri Devaraj Urs Academy of Higher Education and Research , Kolar, Karnataka
On Sep 2018

Dr. Saumya Navit

"As a peer-reviewed journal, the Journal of Clinical and Diagnostic Research provides an opportunity to researchers, scientists and budding professionals to explore the developments in the field of medicine and dentistry and their varied specialities, thus extending our view on biological diversities of living species in relation to medicine.
‘Knowledge is treasure of a wise man.’ The free access of this journal provides an immense scope of learning for the both the old and the young in field of medicine and dentistry as well. The multidisciplinary nature of the journal makes it a better platform to absorb all that is being researched and developed. The publication process is systematic and professional. Online submission, publication and peer reviewing makes it a user-friendly journal.
As an experienced dentist and an academician, I proudly recommend this journal to the dental fraternity as a good quality open access platform for rapid communication of their cutting-edge research progress and discovery.
I wish JCDR a great success and I hope that journal will soar higher with the passing time."

Dr Saumya Navit
Professor and Head
Department of Pediatric Dentistry
Saraswati Dental College
On Sep 2018

Dr. Arunava Biswas

"My sincere attachment with JCDR as an author as well as reviewer is a learning experience . Their systematic approach in publication of article in various categories is really praiseworthy.
Their prompt and timely response to review's query and the manner in which they have set the reviewing process helps in extracting the best possible scientific writings for publication.
It's a honour and pride to be a part of the JCDR team. My very best wishes to JCDR and hope it will sparkle up above the sky as a high indexed journal in near future."

Dr. Arunava Biswas
MD, DM (Clinical Pharmacology)
Assistant Professor
Department of Pharmacology
Calcutta National Medical College & Hospital , Kolkata

Dr. C.S. Ramesh Babu
" Journal of Clinical and Diagnostic Research (JCDR) is a multi-specialty medical and dental journal publishing high quality research articles in almost all branches of medicine. The quality of printing of figures and tables is excellent and comparable to any International journal. An added advantage is nominal publication charges and monthly issue of the journal and more chances of an article being accepted for publication. Moreover being a multi-specialty journal an article concerning a particular specialty has a wider reach of readers of other related specialties also. As an author and reviewer for several years I find this Journal most suitable and highly recommend this Journal."
Best regards,
C.S. Ramesh Babu,
Associate Professor of Anatomy,
Muzaffarnagar Medical College,
On Aug 2018

Dr. Arundhathi. S
"Journal of Clinical and Diagnostic Research (JCDR) is a reputed peer reviewed journal and is constantly involved in publishing high quality research articles related to medicine. Its been a great pleasure to be associated with this esteemed journal as a reviewer and as an author for a couple of years. The editorial board consists of many dedicated and reputed experts as its members and they are doing an appreciable work in guiding budding researchers. JCDR is doing a commendable job in scientific research by promoting excellent quality research & review articles and case reports & series. The reviewers provide appropriate suggestions that improve the quality of articles. I strongly recommend my fraternity to encourage JCDR by contributing their valuable research work in this widely accepted, user friendly journal. I hope my collaboration with JCDR will continue for a long time".

Dr. Arundhathi. S
MBBS, MD (Pathology),
Sanjay Gandhi institute of trauma and orthopedics,
On Aug 2018

Dr. Mamta Gupta,
"It gives me great pleasure to be associated with JCDR, since last 2-3 years. Since then I have authored, co-authored and reviewed about 25 articles in JCDR. I thank JCDR for giving me an opportunity to improve my own skills as an author and a reviewer.
It 's a multispecialty journal, publishing high quality articles. It gives a platform to the authors to publish their research work which can be available for everyone across the globe to read. The best thing about JCDR is that the full articles of all medical specialties are available as pdf/html for reading free of cost or without institutional subscription, which is not there for other journals. For those who have problem in writing manuscript or do statistical work, JCDR comes for their rescue.
The journal has a monthly publication and the articles are published quite fast. In time compared to other journals. The on-line first publication is also a great advantage and facility to review one's own articles before going to print. The response to any query and permission if required, is quite fast; this is quite commendable. I have a very good experience about seeking quick permission for quoting a photograph (Fig.) from a JCDR article for my chapter authored in an E book. I never thought it would be so easy. No hassles.
Reviewing articles is no less a pain staking process and requires in depth perception, knowledge about the topic for review. It requires time and concentration, yet I enjoy doing it. The JCDR website especially for the reviewers is quite user friendly. My suggestions for improving the journal is, more strict review process, so that only high quality articles are published. I find a a good number of articles in Obst. Gynae, hence, a new journal for this specialty titled JCDR-OG can be started. May be a bimonthly or quarterly publication to begin with. Only selected articles should find a place in it.
An yearly reward for the best article authored can also incentivize the authors. Though the process of finding the best article will be not be very easy. I do not know how reviewing process can be improved. If an article is being reviewed by two reviewers, then opinion of one can be communicated to the other or the final opinion of the editor can be communicated to the reviewer if requested for. This will help one’s reviewing skills.
My best wishes to Dr. Hemant Jain and all the editorial staff of JCDR for their untiring efforts to bring out this journal. I strongly recommend medical fraternity to publish their valuable research work in this esteemed journal, JCDR".

Dr. Mamta Gupta
(Ex HOD Obs &Gynae, Hindu Rao Hospital and associated NDMC Medical College, Delhi)
Aug 2018

Dr. Rajendra Kumar Ghritlaharey

"I wish to thank Dr. Hemant Jain, Editor-in-Chief Journal of Clinical and Diagnostic Research (JCDR), for asking me to write up few words.
Writing is the representation of language in a textual medium i e; into the words and sentences on paper. Quality medical manuscript writing in particular, demands not only a high-quality research, but also requires accurate and concise communication of findings and conclusions, with adherence to particular journal guidelines. In medical field whether working in teaching, private, or in corporate institution, everyone wants to excel in his / her own field and get recognised by making manuscripts publication.

Authors are the souls of any journal, and deserve much respect. To publish a journal manuscripts are needed from authors. Authors have a great responsibility for producing facts of their work in terms of number and results truthfully and an individual honesty is expected from authors in this regards. Both ways its true "No authors-No manuscripts-No journals" and "No journals–No manuscripts–No authors". Reviewing a manuscript is also a very responsible and important task of any peer-reviewed journal and to be taken seriously. It needs knowledge on the subject, sincerity, honesty and determination. Although the process of reviewing a manuscript is a time consuming task butit is expected to give one's best remarks within the time frame of the journal.
Salient features of the JCDR: It is a biomedical, multidisciplinary (including all medical and dental specialities), e-journal, with wide scope and extensive author support. At the same time, a free text of manuscript is available in HTML and PDF format. There is fast growing authorship and readership with JCDR as this can be judged by the number of articles published in it i e; in Feb 2007 of its first issue, it contained 5 articles only, and now in its recent volume published in April 2011, it contained 67 manuscripts. This e-journal is fulfilling the commitments and objectives sincerely, (as stated by Editor-in-chief in his preface to first edition) i e; to encourage physicians through the internet, especially from the developing countries who witness a spectrum of disease and acquire a wealth of knowledge to publish their experiences to benefit the medical community in patients care. I also feel that many of us have work of substance, newer ideas, adequate clinical materials but poor in medical writing and hesitation to submit the work and need help. JCDR provides authors help in this regards.
Timely publication of journal: Publication of manuscripts and bringing out the issue in time is one of the positive aspects of JCDR and is possible with strong support team in terms of peer reviewers, proof reading, language check, computer operators, etc. This is one of the great reasons for authors to submit their work with JCDR. Another best part of JCDR is "Online first Publications" facilities available for the authors. This facility not only provides the prompt publications of the manuscripts but at the same time also early availability of the manuscripts for the readers.
Indexation and online availability: Indexation transforms the journal in some sense from its local ownership to the worldwide professional community and to the public.JCDR is indexed with Embase & EMbiology, Google Scholar, Index Copernicus, Chemical Abstracts Service, Journal seek Database, Indian Science Abstracts, to name few of them. Manuscriptspublished in JCDR are available on major search engines ie; google, yahoo, msn.
In the era of fast growing newer technologies, and in computer and internet friendly environment the manuscripts preparation, submission, review, revision, etc and all can be done and checked with a click from all corer of the world, at any time. Of course there is always a scope for improvement in every field and none is perfect. To progress, one needs to identify the areas of one's weakness and to strengthen them.
It is well said that "happy beginning is half done" and it fits perfectly with JCDR. It has grown considerably and I feel it has already grown up from its infancy to adolescence, achieving the status of standard online e-journal form Indian continent since its inception in Feb 2007. This had been made possible due to the efforts and the hard work put in it. The way the JCDR is improving with every new volume, with good quality original manuscripts, makes it a quality journal for readers. I must thank and congratulate Dr Hemant Jain, Editor-in-Chief JCDR and his team for their sincere efforts, dedication, and determination for making JCDR a fast growing journal.
Every one of us: authors, reviewers, editors, and publisher are responsible for enhancing the stature of the journal. I wish for a great success for JCDR."

Thanking you
With sincere regards
Dr. Rajendra Kumar Ghritlaharey, M.S., M. Ch., FAIS
Associate Professor,
Department of Paediatric Surgery, Gandhi Medical College & Associated
Kamla Nehru & Hamidia Hospitals Bhopal, Madhya Pradesh 462 001 (India)
On May 11,2011

Dr. Shankar P.R.

"On looking back through my Gmail archives after being requested by the journal to write a short editorial about my experiences of publishing with the Journal of Clinical and Diagnostic Research (JCDR), I came across an e-mail from Dr. Hemant Jain, Editor, in March 2007, which introduced the new electronic journal. The main features of the journal which were outlined in the e-mail were extensive author support, cash rewards, the peer review process, and other salient features of the journal.
Over a span of over four years, we (I and my colleagues) have published around 25 articles in the journal. In this editorial, I plan to briefly discuss my experiences of publishing with JCDR and the strengths of the journal and to finally address the areas for improvement.
My experiences of publishing with JCDR: Overall, my experiences of publishing withJCDR have been positive. The best point about the journal is that it responds to queries from the author. This may seem to be simple and not too much to ask for, but unfortunately, many journals in the subcontinent and from many developing countries do not respond or they respond with a long delay to the queries from the authors 1. The reasons could be many, including lack of optimal secretarial and other support. Another problem with many journals is the slowness of the review process. Editorial processing and peer review can take anywhere between a year to two years with some journals. Also, some journals do not keep the contributors informed about the progress of the review process. Due to the long review process, the articles can lose their relevance and topicality. A major benefit with JCDR is the timeliness and promptness of its response. In Dr Jain's e-mail which was sent to me in 2007, before the introduction of the Pre-publishing system, he had stated that he had received my submission and that he would get back to me within seven days and he did!
Most of the manuscripts are published within 3 to 4 months of their submission if they are found to be suitable after the review process. JCDR is published bimonthly and the accepted articles were usually published in the next issue. Recently, due to the increased volume of the submissions, the review process has become slower and it ?? Section can take from 4 to 6 months for the articles to be reviewed. The journal has an extensive author support system and it has recently introduced a paid expedited review process. The journal also mentions the average time for processing the manuscript under different submission systems - regular submission and expedited review.
Strengths of the journal: The journal has an online first facility in which the accepted manuscripts may be published on the website before being included in a regular issue of the journal. This cuts down the time between their acceptance and the publication. The journal is indexed in many databases, though not in PubMed. The editorial board should now take steps to index the journal in PubMed. The journal has a system of notifying readers through e-mail when a new issue is released. Also, the articles are available in both the HTML and the PDF formats. I especially like the new and colorful page format of the journal. Also, the access statistics of the articles are available. The prepublication and the manuscript tracking system are also helpful for the authors.
Areas for improvement: In certain cases, I felt that the peer review process of the manuscripts was not up to international standards and that it should be strengthened. Also, the number of manuscripts in an issue is high and it may be difficult for readers to go through all of them. The journal can consider tightening of the peer review process and increasing the quality standards for the acceptance of the manuscripts. I faced occasional problems with the online manuscript submission (Pre-publishing) system, which have to be addressed.
Overall, the publishing process with JCDR has been smooth, quick and relatively hassle free and I can recommend other authors to consider the journal as an outlet for their work."

Dr. P. Ravi Shankar
KIST Medical College, P.O. Box 14142, Kathmandu, Nepal.
On April 2011

Important Notice

Year : 2007 | Month : August | Volume : 1 | Issue : 4 | Page : 339 - 346

Multi Hit, Dropoff Percentage and NCM-2: Three Improvements in BLAST


Computer Science Department, Thapar University, Patilala-147004, India

Correspondence Address :
Dr Deepak Garg,Computer Science Department, Thapar University,
Patilala-147004, India. Email :, Ph: +91-9815599654


Various algorithms are in use in medical processes to improve the speed, sensitivity and accuracy of the computations and analyses involved in those experiments.
The aim of this paper is to suggest three improvements, namely Multi Hit, Dropoff percentage and NCM-2 in the BLAST algorithm.
BLAST (Basic Local Alignment Search Tool) is a popular tool used for determining the patterns in genomic sequences. As the data is increasing exponentially, the need for advanced and complex algorithms for improving the accuracy, speed and sensitivity of pattern discovery tools in bioinformatics is also increasing.
First Improvement: The initialization of the word matches in a pairwise sequence alignment works either on single hit or two-hit algorithms. Instead, if we use a 3-hit or n-hit in general then the results improve in general and improve dramatically for some specific species and sequences.
Second Improvement: BLAST is using a drop-off score to calculate the highest scoring pairs between two sequences. A change has been proposed to calculate the threshold score that determines the inclusion of the subsequence in the result. Instead of using a drop-off score, if we use a drop-off percentage, it gives better results for some sequences.
Third Improvement: We propose an NCM-2 approach for normalizing BLAST values for simple regions. This approach is based upon the natural properties of the Amino acid sequences. The algorithms have been run on Linux ES platform with Compaq Presario 2GB RAM and compared to the original BLAST.

Nowadays, medical practitioners are increasingly relying on sequence comparison tools to understand the various properties of the genomes under consideration. BLAST is being used for pairwise alignments instead of multisequence alignments. BLAST can perform local as well as global alignments.

In case of global alignments, it sacrifices some of the advantages of the local alignments. It is the most popular tool being used by the biologists and by people involved in the clinical trials of various drugs. Detection of the SARS disease source and then finding a remedy for it is a good example of success of BLAST-like tools.

These kinds of algorithms are also being used in pulse oximetry to remove the background noise. These tools have been used for solving various other medical problems. The examples and references are available at NCBI [].

The central idea of the BLAST algorithm is that a statistically significant alignment that will be of use to the doctors is likely to contain a high-scoring pair of aligned words. BLAST first scans the database of genomes for words that score at least T when aligned with some word within the query genome sequence. Any aligned word pair satisfying this condition is called a `hit`. In the second part, BLAST checks whether each hit lies within an alignment with a score sufficient for the sequence to be part of the result set. It will be achieved by extending a hit in both directions until the running alignment’s score has dropped more than X below the maximum score yet attained. This extension step is computationally quite expensive. The extension step typically accounts for two third time of BLAST execution time. It is therefore desirable to reduce the number of extensions performed (1),(2).

A two-hit algorithm was made to solve this problem. It is observed that an HSP (High Scoring Pairs) of interest is much longer than a single word pair and may therefore entail multiple hits on the same diagonal. The multiple hits should be in relatively short distance of one another. Specifically, a window length A is chosen, and it invokes an extension only when two non-overlapping hits are found within the distance A of one another on the same diagonal. Any hit that overlaps with the most recent one is ignored. We require two hits rather than one to invoke an extension. Therefore, the threshold parameter T must be lowered to retain comparable sensitivity. The effect is that many more single hits are found, but only a small fraction has an associated second hit on the same diagonal that triggers an extension. The great majority of hits may be dismissed after the minor calculation of looking up, for the appropriate diagonal, the co-ordinate of the most recent hit. After checking whether it is within distance A of the current hit’s coordinate, the old is finally replaced with the new co-ordinate. Empirically, the computation saved by requiring fewer extensions more than offsets the extra computation required to process the larger number of hits.

Multi hit
There are very rare chances that the occurrence of disease patterns will only be at one or two places in the genome sequence. Generally, it will be spread at various places in the genome sequence. When we look up the database with the query sequences to find some similarity between the sequence under scrutiny and the other sequences present in the database, the result will have the details of any functional or relational match between the two (3),(4).

The proposed new approach extends a two-hit algorithm to an N-hit algorithm. Here, the value of N can be given by the user, depending upon the requirements. The value of N will then act as a tradeoff between speed and sensitivity. According to the N-hit algorithm, we can choose a window length A. The algorithm step invokes an extension only when N non-overlap

Material and Methods

A test set was constructed by selecting the 15 families from the Pfam database that are high in ranking. The Pfam has about 5000 protein families. Forty protein sequences from these families were chosen randomly. This made up a total of 600 sequences. This test set contains fragments as well as full protein sequences. Some proteins have multiple domains and some do not have any domain at all.

This data set has both protein fragments and full protein sequences. The SEG was run with the parameter values W = 12, K(1) = 2.2 bit and K(2) = 2.5 bit. The threshold score was 40 for CAST. The cutoff = 0.01, max-search offset =4 and min-search-offset=1 was used for XNU.
XNU, SEG and CAST use masking operations. Here, DR represents the detection ratio and is calculated as
DR = (Number of domains in masked sequence/ Number of domains in unmasked given sequence) * 100
HR represents Hit ratio and is calculated as
HR = (number of masked residues outside the domains of the sequence/number of masked residues in the filtered sequence) * 100


The objective of filtering is to mask non-domain regions without masking the domain regions. The detection ratio may decrease by masking the domain regions. We get a maximum detection ratio. NCM-2 does not have any masking operation and the Pfam database entries themselves have their domains identified with the algorithm inbuilt into them. Therefore, NCM-2 detects 100% of the simple regions. Any algorithm without masking will identify 100% of the sequences. The objective of masking was to filter out high scoring database subsequences coming in the result of the alignment showing higher similarity. The same task is now being performed by the semantic introduced above. It is based on the composition of the sequence and also depends on the number of matches, mismatches, neutral matches and conservative matches. Time is saved because there is no need to perform the masking operation. The same saving in time can be utilized to calculate the probabilities related to C,N,M+,M- of NCM-2. As shown in Table/Fig 4], NCM-2 will detect 100 percent of the sequences due to non masking as compared to XNU(97.2 ), SEG (93.4 ), CAST(98.4). This method also takes care of the non-genuine sequences and eliminates them from the list of significant matches.


By introducing the new approach of multi-hit with drop off percentage, there was a significant improvement in the running time of BLAST. The biologist also has the flexibility to get the result of his own choice by changing either the value of the number of hits or the drop off percentage or both. The introduction of multiple hits will have an effect on the sensitivity if the number of hits selected is more. In the case of three hits, the algorithm shows an improvement ranging from 11 to 26 percent on different sequences. The introduction of the drop off percentage results in less number of calculations because there is no need to go to the scoring matrix and the resulting improvement ranges from 1 to 5 percent. The combined algorithm implementation of multi-hit with drop off percentage shows an improvement in the range of 7 to 21 percent. Therefore, using this method, the biologist can derive the dual benefits of flexibility and speed without compromising on any other aspect. Due to NCM-2 no information will be lost and genuine sequences will travel to the result of the homology searches.


Golding GB. Simple sequence is abundant in eukaryotic proteins. Protein Science 1999;8:1358-1361.
Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National academy of sciences USA 1990;87:2264-2268.
Karlin S, Altschul SF. Applications and statistics for multiple high scoring segments in molecular sequences. Proceedings of the National academy of sciences USA 1993;90:5873-5877.
Dembo A, Karlin S. Strong limit theorems of empirical functional for large exceedances of partial sums off i.i.d variables. Ann Prob 1991;19:1737-1755.
Dembo A, Karlin S, Zeitouni O. a and b Critical Phenomena for sequence matching with scoring and Limit distribution of maximal non-aligned two sequence segmental score. Ann Prob1994;22:1993-2021, 2022-2039.
Claverie JM, States DJ. Information enhancement methods for large scale sequence analysis.Computers and Chemistry 1993;17,191-201.
Wooton JC. Sequences with unusual amino acid compositions Current Opinion in Structural Biology 1994;4:413-421.
Yona G, Levitt M. 2000. A unified sequence structure classification of proteins: combining sequence and structure in a map of protein space. Proc Recomb 2000; 308-317.
Promponas et. Al. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics 16; 915-922.
. Claverie JM, States DJ. Information enhancement methods for large scale sequence analysis. Comput Chem 1993;17:191-201.
. Gusfield D. Algorithms on strings, trees and sequence. Algorithms on Strings, trees and sequences, Cambridge University Press 1990. NY. PP. 89-107.

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