1.Comparing the use of Google Scholar, HighWire Press and Scirus in finding a frequently used protocol for RNA isolation from human testes, for microarray experiments.

RNA isolation method

Google Scholar

HighWire Press

Scirus

PubMed*

Trizol

4

3

-

9

RNeasy kit

1

2

-

4

Single-step extraction

-

-

-

1

RNAqueous-4PCR kit

-

-

-

1

Purchased

-

1

-

3

 
Macherey & Nagel kit

1

-

-

2

Tri reagent

1

1

-

1

 
Guanidine-isothiocyanate procedure

-

-

-

1

QuickPrep Micro mRNA purification kit

1

-

-

-

RNX plus solution

1

-

-

-

Others

-

1

-

-

1. The numbers represent the no. of hits mentioning a particular method. First 100 hits from the obtained results were analyzed in case of each tool except PubMed (hits were <100).

2. A complicated set of queries were designed to target the citation fields in case of PubMed and were then used in combination. This exercise was time consuming and tedious compared to the use of other full-text scanners (for details on the required type of query, refer note 3 at the end of the document).

2. Comparison of Google Scholar, HighWire Press and Scirus for finding RNA isolation protocols involving trizol used in microarray work


Google Scholar

HighWire Press

Scirus

PubMed*

RNA isolation using trizol

6

4

2

0

No. of hits analyzed: 20 per tool

The query set used for PubMed in this case was equivalent to that of the other tools.

3. Comparing the use of Google Scholar, HighWire Press and Scirus in finding the most frequently used primer designing programs.

Google Scholar

HighWire Press

Scirus

PubMed Central

Queries

Std. query*

Mod. query**

Std. query*

Std. query*

Limits applied

Subject areas: Biology, Life Sciences, and Environmental Science
2007 - 2009

Journal source: All (including Pubmed)
2007 - 2009

Journal sources: Pubmed / Medline, BioMed Central, ScienceDirect, Scitation, Pubmed Central; Information type: Articles
Jan2007 - Dec2009

Article type : Any of these article types (OR)

Include : Show any articles that are free in PMC now.

2007 - 2009

Total hits

399

110

51

16104

Primer designing tools detected from citations

% relevant hits

Primer 3***

18

18

9

11

Primer express***

9

17

11

3

Beacon designer

1

3

9

-

Vector NTI

3

5

3

-

CODEHOP

3

1

4

-

OLIGO

1

2

4

-

Oligo 6.0 software (Molecular Biology Insights Inc., Cascade, CO, USA)

2

4

1

-

Clone Manager version 8 (SciEd Software).

3

1

2

-

Lasergene software/DNASTAR/Primer select

2

2

1

1

Primer Quest

1

4

-

-

Biology workbench 3.2 Tm

2

3

-

-

Primer Premier™ (Integrated DNA Technologies)

-

-

4

-

Primer Premier v5.0

-

-

4

-

FastPCR software

2

2

-

-

GenoFrag

3

1

-

-

Consed graphical tool version 14

-

-

4

-

Total % relevant hits#

64

84

60

22

The no. of hits represents the average number of articles obtained from the 2 queries performed independently by two individuals.

1.Std. query (average of results from the following two queries):

query 1 - "primers designed using" AND (software OR tool OR program OR suite OR softwares OR tools OR programs)

query 2 - “used to design primer” AND (software OR tool OR program OR suite OR softwares OR tools OR programs)

2.Mod. Query (average of results from the following two queries):

query 1 - "primers designed using" AND (software* OR tool* OR program OR programs)

query 2 - “used to design primer” AND (software* OR tool* OR program OR programs)

Primer 3 and primer Express software seem to be the most used software in the recent times.

This indicates the total number of relevant hits, that is inclusive of some software not mentioned in the table (the tools referred to at least twice, are shown here).