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pdf2020 Annual BLAST User Survey
OMB Control Number: 0925-0648
Expiration Date: 05/31/2021
Public reporting burden for this collection of information is estimated to average 7 minutes per
response, including the time for reviewing instructions, searching existing data sources,
gathering and maintaining the data needed, and completing and reviewing the collection of
information. An agency may not conduct or sponsor, and a person is not required to respond
to, a collection of information unless it displays a current valid OMB control number.
Send comments regarding this burden estimate or any other aspect of this collection of
information, including suggestions for reducing this burden, to NIH, Project clearance Branch,
6705 Rockledge Drive, MSC 7974, Bethesda, MD 20892-7974, ATTN: PRA (0925-0648). Do
not return the completed form to this address.
Page 1 of 15
Q1 Which professional categories best describes you? (Please select one.) *
o Bioinformatics professional (1)
o Educator (2)
o Healthcare professional (3)
o Librarian / Information Specialist (4)
o Life Science Researcher (5)
o Student (6)
o Technician (7)
o Computer Scientist / Software Developer (8)
o
Other (Please specify below.) (9)
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Q2 Which of the following categories best describes your organization? *
o College or University (1)
o Commercial / Industry (2)
o Non-profit Organization (3)
o Research Institute (4)
o Government (5)
o Hospital/health organization (6)
o
Other (Please specify below.) (7)
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Page 2 of 15
Q3 How frequently do you use each of the following services on the BLAST web service
(https://blast.ncbi.nlm.nih.gov/)?
Daily (1)
Weekly (2)
Monthly (3)
Infrequently
(4)
Never (5)
Nucleotide
BLAST
(blastn) (1)
o
o
o
o
o
Protein
BLAST
(blastp) (2)
o
o
o
o
o
Translated
BLAST
(blastx,
tblastn,
tblastx) (3)
o
o
o
o
o
Align two or
more
sequences
(4)
o
o
o
o
o
o
o
o
o
o
o
o
o
o
o
PrimerBLAST
(5)
IgBLAST (6)
Page 3 of 15
Q4 Why do you use BLAST? (Please select all that apply.)
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Identify unknown mRNA transcripts (1)
Identify unknown proteins (2)
Annotate novel genomic sequences (3)
Search for homologs in other organisms (4)
Identify organisms (taxa) in environmental / metagenomic samples (5)
Screen for contamination (6)
Designing/Screening Primers (7)
Verify the identity of the source organism (8)
Verify the corresponding gene for a query sequence (9)
Map reads to a genome (10)
Education/Instruction (11)
Other (Please specify below.) (12)
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Q5 Do you run BLAST searches for others in your organization, for example you do this as a
service for others?
o Yes (1)
o No (2)
Page 4 of 15
Q6 How frequently do you search with multiple of sequences?
o Daily (1)
o Weekly (2)
o Monthly (3)
o Infrequently (4)
o Never (5)
Q7 Which BLAST services do you use? (Please select all that apply.)
▢
▢
Not applicable (I do not use any of these services) (1)
Use the BLAST website and upload files and/or paste one or more sequences in
the sequence field (2)
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Use the BLAST+ applications on the command line remote to submit BLAST
searches to NCBI (3)
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Use the BLAST+ applications on the command line with my own/custom
databases (4)
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Use the BLAST+ applications on the command line with BLAST
databases/FASTA provided by NCBI (5)
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Submit BLAST searches using scripts that access the BLAST URL API (6)
Use NCBI BLAST+ docker image from dockerhub (7)
Use BLAST on the cloud. (Please specify provider below.) (8)
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Use BLAST through a third-party software. (Please specify name of software
below.) (9) ________________________________________________
Page 5 of 15
Q8 How frequently do you use the standalone BLAST+ (command line) applications? *
o Daily (1)
o Weekly (2)
o Monthly (3)
o Infrequently (4)
o Never (5)
Following questions with display logic will only appear if anything but “Never” is selected in Q8
Display This Question:
If How frequently do you use the standalone BLAST+ (command line) applications? * = Daily
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Weekly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Monthly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Infrequently
Q9 Why do you use BLAST+ versus BLAST web service?
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Display This Question:
If How frequently do you use the standalone BLAST+ (command line) applications? * = Daily
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Weekly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Monthly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Infrequently
Q10 Why do you use BLAST+ Docker versus BLAST+?
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Page 6 of 15
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Display This Question:
If How frequently do you use the standalone BLAST+ (command line) applications? * = Daily
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Weekly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Monthly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Infrequently
Page 7 of 15
Q11 Please indicate how strongly you agree or disagree with the following statements about the
standalone BLAST+ applications.
Strongly
agree (1)
Agree (2)
Neither
agree nor
disagree
(3)
Disagree
(4)
Strongly
disagree
(5)
N/A (6)
I am
satisfied
with the
performance
of the
BLAST+
applications
(1)
o
o
o
o
o
o
I frequently
look at the
databases
available to
see if there
is a better
one for me
to use (2)
o
o
o
o
o
o
Available
formatting
options work
well for me
(3)
o
o
o
o
o
o
I have an
automated
task that
downloads
the latest
databases
(4)
o
o
o
o
o
o
Page 8 of 15
Display This Question:
If How frequently do you use the standalone BLAST+ (command line) applications? * = Daily
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Weekly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Monthly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Infrequently
Q12 If there was one thing you could change about BLAST+, what would it be?
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Display This Question:
If How frequently do you use the standalone BLAST+ (command line) applications? * = Daily
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Weekly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Monthly
Or How frequently do you use the standalone BLAST+ (command line) applications? * = Infrequently
Q13 Do you use BLAST+ as part of an automated pipeline?
o Yes (1)
o No (2)
Display This Question:
If Do you use BLAST+ as part of an automated pipeline? = Yes
Page 9 of 15
Q14 When running BLAST+ as part of an automated pipeline what databases do you
use? (Please select all that apply.)
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▢
Pre-formatted BLAST database (nr, nt, others from BLAST FTP site) (1)
Pre-formatted BLAST database (nr, nt, others from cloud service provider –
GCP, AWS) (2)
▢
▢
Other NCBI databases
(3)
Your own databases (4)
Display This Question:
If Do you use BLAST+ as part of an automated pipeline? = Yes
Q15 When using this pipeline which of the following do you use? (Please select all that apply.)
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Python (1)
Amazon Web Service (2)
Google Cloud Platform (3)
Bash (4)
PERL (5)
Common Workflow Language (CWL) (6)
Docker (7)
GitHub (8)
NCBI EDirect or E-Utilities (9)
The BLAST URL API (10)
Other (Please specify below.) (11)
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Page 10 of 15
Display This Question:
If Do you use BLAST+ as part of an automated pipeline? = Yes
Q16 What features, or changes would you like to make to BLAST+ so it better supports your
pipeline needs?
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Page 11 of 15
Q17 Please indicate how strongly you agree or disagree with the following statements about the
BLAST web service.
Strongly
agree (1)
Agree (2)
Neither
agree nor
disagree
(3)
Disagree
(4)
Strongly
disagree
(5)
N/A (6)
Knowing which
BLAST
databases to
choose is easy.
(1)
o
o
o
o
o
o
Finding BLAST
databases for a
specific
organism is
easy. (2)
o
o
o
o
o
o
Finding BLAST
databases for a
specific
genome is
easy (3)
o
o
o
o
o
o
BLAST results
are returned
quickly. (4)
o
o
o
o
o
o
BLAST results
are easy to
read and
understand.
(5)
o
o
o
o
o
o
Downloading
my results is
easy and
provides what I
need. (6)
o
o
o
o
o
o
The
Descriptions
table has a
clear and
understandable
layout. (7)
o
o
o
o
o
o
The
Descriptions
table has all
the fields I
need. (8)
o
o
o
o
o
o
Page 12 of 15
Q18 Please provide any specific fields or links you would add to the Descriptions table.
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Q19 Would you be interested in a BLAST web service where you enter your task, such as
“Search for homologs in other organisms”; then enter your sequence and then hit Go. BLAST
will then select the appropriate database and present your results?
o Yes (1)
o No (2)
Q31 Comments or feedback about the web service above.
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Page 13 of 15
Q20 Would you be interested in a database clustered by % identity, derived from nt or nr which
would significantly reduce redundancy and improve search times?
o Yes (1)
o No (2)
Q32 Comments or feedback about the database above.
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Q23 Please provide any additional type of formats/images that you would want to save/print.
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Page 14 of 15
Q24 On a scale from 0-10, how likely are you to recommend BLAST to a friend or colleague? *
o 0 (0)
o 1 (1)
o 2 (2)
o 3 (3)
o 4 (4)
o 5 (5)
o 6 (6)
o 7 (7)
o 8 (8)
o 9 (9)
o 10 (10)
Q25 If there was one thing you could change about the BLAST web service, what would it be?
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Q26 If you would like to provide more feedback, please contact us at [email protected]
Page 15 of 15
| File Type | application/pdf |
| File Title | 2020 Annual BLAST User Survey (NDB-233) |
| Author | Qualtrics |
| File Modified | 2020-11-04 |
| File Created | 2020-10-28 |