poster2010x - UCO Department of Computer Science

crashclappergapΛογισμικό & κατασκευή λογ/κού

13 Δεκ 2013 (πριν από 3 χρόνια και 10 μήνες)

70 εμφανίσεις

Linux Platform


Download the source tar ball from the
BLAST source code link


ncbi
-
blast
-
2.2.24+
-
src.tar.gz



Compilation


cd

/
BLASTdirectory
/
c++


./configure
--
without
-
debug
--
with
-
mt

--
with
-
build
-
root=
ReleaseMT


cd

ReleaseMT
/build


make
all_r







After compilation:


Run Perl update_blastdb.pl
database_name

to download a selected database
(ex.
htgs
,
refseq_rna
)


Conduct a test of BLAST’s installation
for some standard nucleotide
similarity search


Type

./
blastdbcmd

-
db
database_name

-
entry
nm_000249
-
outfmt

"%f"
-
out test_query.txt


blastdbcmd


takes a selected database (
-
db),
a
search string parameter (
-
entry), output
format (

outfmt
) , and output file (
-
out)


Finds a sequence from
-
db based upon
search criteria, and then place the sequence
into output file using the give format


Type ./
blastn

-
query my_query.txt
-
db
refseq_rna

-
out ouput.txt


blastn

takes
a sequence input file (
-
query),

a
selected database (
-
db)
, and output file (
-
out)



Runs a nucleotide query search on the
given

db, then save its results in output file



Compile and Run BLAST Locally from Source Code

Department of Computer Science


College of Mathematics & Science


Preston Cofield

Advisor: Gang Qian


ABSTRACT
:

BLAST

is

a

widely
-
used

search

tool

for

homology

detection

in

large

biological

sequence

databases
.

In

this

presentation,

we

provide

a

guidance

of

locating

BLAST

source

code

on

NCBI

and

download

it

to

a

local

computer
.

We

will

then

show

the

compilation

and

execution

of

BLAST

programs

on

both

Linux

and

Windows

platforms
.

Using

BLAST,

locally,

allows

study

of

the

structure

and

algorithms

of

the

BLAST

source

p r o g r a m s

so

that

comparison

research

on

improving

search

performance

on

biological

sequence

databases

can

be

conducted
.


Introduction


Basic Local Alignment Search Tool
(BLAST)
[1,2,3]

is a popular search
algorithm in bioinformatics, useful
in analyzing homologous
comparisons between biological
sequences


BLAST can be run in two ways:

1.
A Web interface provided by the
National Center for
Biotechnology Information
(NCBI)

2.
Running BLAST on a local
computer



Running BLAST locally offers


great flexibility to its users


BLAST’s Source code link:


ftp://ftp.ncbi.nlm.nih.gov/blast/execut

ables
/blast+/LATEST/


Databases Download link:


ftp://ftp.ncbi.nlm.nih.gov/blast/db/


Windows Platform


Download an MSI from the download link


Windows (32
-
bit x86, MSI installer)



After installation:


Windows OS needs the ability to run Perl
scripts



Run Perl update_blastdb.pl
database_name

to download a selected database
(ex.
htgs
,
refseq_rna
)









All BLAST programs are ran from the
command prompt


Perform a test of BLAST’s installation for
some standard nucleotide
similarity search


Create a new OS environment variable
holding the full path to the BLAST’s bin


Facilitates inputting BLAST commands


In an open command prompt, enter the
BLAST directory:


Type

blastdbcmd

-
db
database_name

-
entry
nm_000249
-
outfmt

"%f"
-
out test_query.txt


blastdbcmd


takes a selected database (
-
db), a
search string parameter (
-
entry), output format (

outfmt
) , and output file (
-
out)


Finds a sequence from
-
db based upon search
criteria, and then place the sequence into output file
using the give format


Type
blastn

-
query my_query.txt
-
db
refseq_rna

-
out
ouput.txt


blastn

takes
a sequence input file (
-
query),

a
selected database (
-
db)
, and output file (
-
out)



Runs a nucleotide query search on the given

db,
then save its results in output file







Results
and Conclusion


Linux Platform


Creation of an output file containing the
search results from the
blastn

function









Windows Platform


Creation of an output file containing the
search results from the
blastn

function









Since BLAST can be compiled, and run
locally by the user, the user gains the
capability to further study, and improve
upon BLAST’s heuristic algorithms


References

[1] BLAST Main Web site:
http://blast.ncbi.nlm.nih.gov/Blast.cgi

[2]
Altschul

S, Gish W, Miller W, Myers E and
Lipman

D. Basic local alignment search tool.
J. Molecular Biology 1990; 215(3):403
-
410.

[3]
Altschul

S, Madden T,
Schäffer

A, Zhang J,
Zhang Z, Miller W and
Lipman

D. Gapped
BLAST and PSI
-
BLAST: a new generation of
protein database search programs. Nucleic
Acids Research 1997; 25(17):3389
-
3402.