MUTIPLE SEQUENCE ALGINMENT TOOLS
COBALT, webPRANK, DbClustal
Kamer Burak *
Dept. of Molecular Biology and Genetics
Izmir Institute of Technology
Izmir, Turkey
kamerisci@std.iyte.edu.tr
Cem TOSUN*
Dept. of Molecular Biology and Genetics
Izmir Institute of Technology
Izmir, Turkey
cemtosun@std.iyte.edu.tr
Bita SABET*
Dept. of Molecular Biology and Genetics
Izmir Institute of Technology
Izmir, Turkey
bitasabet@std.iyte.edu.tr
Abstract—Multiple following alignment tools provide opportunities to confound sequence similarities of two and greater quantity biological sequences such as DNA, RNA or proteins. Wide dispose in order of MSA tools help to come by any needed information and compare them to continue in use results with precision as much of the same kind with possible. This study aims to make known to about general working principles of three multiple order of succession alignment tools; COBALT, webPRANK and DbClustal and compare their results internally also with harvested land other. Index Terms—COBALT, webPRANK, DbClustal
Introduction
Sequence alignment of couple or more biological sequences, which may belong to protein, DNA or RNA is called multiple order of succession alignment (MSA) [1]. Generally multiple sequence alignment is used to identify evolutionary kinship by shares of lineages and descending to often met with ancestor. Thus, computational algorithms are used to manufacture and analyze the alignments.
Most MSA tools conversion to an act heuristic methods rather than global optimization because of computationally expensiveness of describing the optimal alignment betwixt more than a few sequences of assuage length. There are two main approaches to MSA, what one. include progressive and iterative. Progressive multiple alignment course begins with a sequence and progressively aligns the others some by one creating a distance matrix and guide tree from the matrices, which is used to make the resolution the next sequence to be added to the alignment. Progressive MSA is a faster approximate when compared to pair-wise alignment to multiple sequences,...
MUTIPLE SEQUENCE ALGINMENT TOOLS
COBALT, webPRANK, DbClustal
Kamer Burak *
Dept. of Molecular Biology and Genetics
Izmir Institute of Technology
Izmir, Turkey
kamerisci@std.iyte.edu.tr
Cem TOSUN*
Dept. of Molecular Biology and Genetics
Izmir Institute of Technology
Izmir, Turkey
cemtosun@std.iyte.edu.tr
Bita SABET*
Dept. of Molecular Biology and Genetics
Izmir Institute of Technology
Izmir, Turkey
bitasabet@std.iyte.edu.tr
Abstract—Multiple succession alignment tools provide
opportunities to ascertain to be the same sequence similarities of two and
further biological sequences such as DNA, RNA or proteins.
Wide pass near of MSA tools help to induce any needed information
and compare them to achieve results with precision as much being of the kind which
possible. This study aims to inspire about general working
principles of three multiple arrangement alignment tools;
COBALT, webPRANK and DbClustal and bring into comparison their
results internally also with one and the other other.
Index Terms—COBALT, webPRANK, DbClustal
Introduction
Sequence alignment of two or more biological
sequences, which may belong to protein, DNA or RNA is
called multiple following alignment (MSA) [1]. Generally
multiple succession alignment is used to identify evolutionary
connection by shares of lineages and descending to used by all
ancestor. Thus, computational algorithms are used to make
and analyze the alignments.
Most MSA tools use heuristic methods rather than
global optimization for of computationally
expensiveness of describing the optimal alignment between
more than a few sequences of repress length. There are two
main approaches to MSA, that include progressive and
iterative. Progressive multiple alignment process begins with
a sequence and progressively aligns the others undivided by one
creating a distance matrix and govern tree from the matrices,
which is used to make the resolution the next sequence to be added to
the alignment. Progressive MSA is a faster draw near when
compared to pair-wise alignment to multiple sequences,
what one. could be very slow for a small in number sequences [2].
COBALT
One of the latest algorithms to subsist announced is
COBALT (constraint-based alignment tool). COBALT
permits the user to embark in constraints, which the user can
without circumlocution identify. And also the user be possible to ask COBALT to
provide the constraints, what one. is using sequence similarity,
CDD searches and PROSITE (protein-motif database)
prototype searches. Besides, COBALT will alternatively cast
partial profiles based on any CDD (conserved empire
database) search result [3]. Additionally, CDD moreover contains
standby information, which allows forming prejudiced profiles
for input sequences before the inauguration of progressive
alignment. This situation provides computationally cheaper
procedures with regard to building profiles.
* The authors contributed equally to this labor.
As we searched that COBALT has a inexact
framework by using progressive multiple alignments, in
rule to incorporate pairwise constraints from not the same
sources into a multiple alignment. COBALT is used barely for
high scoring consistent subset, what one. also can be called
consistent of put of constraints in case all of the constraints in
the sect could be concurrently fit a multiple alignment [4].
COBALT uses ~y all-vs.-all collection of pairwise
constraints to appear each group of conserved columns. These
columns may contain gaps. However, sequences that contain
gaps in a conserved array of less front than depth don’t join in pairwise constraints
on the side of that column. Thus, these conserved columns are used since
most profile-profile alignments. COBALT finds pairwise
constraints reproduced from database inquire after, combines these
found pairwise constraints and incorporates them into
advancing multiple alignment.
Researchers showed constraints derived from the
CDD and PROSITE are used in method to improve COBALT’s
alignment station. And also they found out that COBALT
has rational runtime performance and alignment accuracy.
The alignments reported ~ dint of. different alignment algorithms
vary significantly that property the importance of conception
[5]. The runtime playing of COBALT is highly based
in c~tinuance data, but experimental it is two times slower than
MUSCLE comparing to ProbCons and PCMA. Thus,
COBALT shows a expert agreement between alignment
quality and runtime of necessity [5]. Apart from these features, the
COBALT algorithm is uniform to other progressive multiple
alignment tools. To generate constraints, alignments are
found and congruous set of constraints and partial profiles are
place to generate guide tree. A multiple alignment is created
by using the current set of constraints and conductor tree. After
creation of bipartitions and realign, finesse is performed
by determining a recent set of constraints. Most of the
sublimation of COBALT was done using BaliBase 2.0 [6];
including 265 alignments branched into 8 sets according to
following length and percent similarity.
webPRANK
WebPRANK is a stochastic multiple alignment tool
for amino-acid, codon and DNA sequences. This program
gives resulting alignment in manifold formats. WebPRANK
compares the evolutionary distances between sequences in
phylogenetics. WebPRANK helps users to light upon structure of
sequence then finds the structural units’ locations in the
sequences [8]. WebPRANK procures every interactive interface
providing the users to temper their multiple sequence
alignment by changing the series of phylogeny [9].
When the users uploaded the series to WebPRANK, it
makes a slow alignment and shows the alignment. It gives
a advantage result with small sequences. Screening and practice of
phylogeny-aware multiple sequence alignment is affluent by
web interface in the WebPRANK server [10].
The WebPRANK server depends up~ the PRANK
phylo-geny-aware multiple series alignment software and
it is executed in C++. This program works from European
Bioinformatics Institute’s computation cluster using Web
Services [10, 11]. Interface of The WebPRANK is JavaScript
and HTML digest. Its server uses the XML. Information of
alignment projection was able to store by this program.
DbClustal
The the bulk reason DbClustal [12] differs from other
multiple sequence alignment tools is its capacity to compound
both local and global alignment algorithms in a tree-based
air. This feature leads to visualizing the greatest number scored
sequences of the Blast database automatically in a shorter
time.
DbClustal is a modified translation of global alignment
program ClustalW cooperated through any local alignment in-
formation so as Ballast, which is a Blast place-processing
program. ClustalW incorporates searching results of a topical
alignment, which are a list of security points found by BLAST
in the database.
The programming speech used in writing of
ClustalW is ANSI C, this trait helps collaboration with
other programs using the corresponding; of like kind language such as Ballast. Ad-
dition of unused modules to ClustalW reveals a strange tool, Db-
Clustal.
The duty of local alignment tool is gathering the
pairs of ungapped segments cast by BLAST and create a
side face of gapped alignments with E-values smaller quantity then 0,1.
BLAST is additional preferred than other members of its house
such as PSI-BLAST because it contains one as well as the other DNA and
protein databases also it is ingenious to find closer homologues,
PSI-BLAT merely includes protein database and it searches as being
distant homologues. The chosen local alignment tool have a mind
give a list of anchor points of the inquiry sequence with top
scoring database sequences. The discovery anchors are only
database sequences, which are relevant to query sequence.
DbClustal generates anchors of entirely sequences. The
overlapping of two anchors of couple database sequences causes
a new defence.
The input of DbClustal should comprise a file of
unaligned sequences and security file of the local alignment
tool. DbClustal gathered complaint of different sources and
automatically integrated them to the global multiple
alignment.
Summary
Multiple series alignment (MSA) is a general
draw near which gives rise to align pair or more biological
* The authors contributed equally to this be.
sample sequences consist of DNA, protein or RNA and in this
critique, we aimed to identify three variant multiple sequence
alignment tools which are improving and used for creation of
evolutionary kinship for guide trees. And we explained
DbClustal, COBALT and WebPRANK MSA tools according
to their discriminating features.
COBALT (constraint-based alignment tool) is some of
the latest progressive algorithms that deduct creation of partial
profiles based adhering conserved domain database to align multiple
sequences.
WebPRANK has a unsullied interface and algorithm that
is excessively easy to use and free program to remark multiple sequence
alignment.
As a ClustalW based alignment, DbClustal is a
processing tool because sequences, which are found by BLAST
protein close. DbClustal creates a multiple sequence
alignment by using the anchor points found ~ the agency of BLAST.
Two of chosen programs; DbClustal and
WebPRANK are tree-based developing programs and
COBALT is a incarceration-based tool, they also have wrangle-
ences such as runtime, interface and severe correctness according to
alignment sizes. COBALT’s runtime performance is highly
depend on data in like manner it can be a bit slower than other MSA tools
only this present compromise between alignment humor and
runtime makes COBALT a capital choice when using multiple
tools is not preferred [13]. Guide-tree prepared ~ the agency of any mem-
ber of Clustal alignment line of ancestors is based on estimated dis-
tance betwixt the sequences. DbClustal uses protein BLAST
inquire results and align them with ClustalW2, which is a
suitable choice for mean size alignments [14].
WebPRANK as well in the manner that providing an interactive web-inter-
audacity takes a chance to reordering the branches of tree to re-
calculated the alignment. During operating with small align-
ments contain small in number sequences WebPRANK will be a religious
choice [14].
Materials & Methods
Before starting to exercise MSA tools we had to prepare
appropriate facts (FASTA format without dashes) so we employment
jalview to convert msf files (msf files were attentive only in
BAliBASE data set) to FASTA toothed. As our FASTA files
were include dashes, we delete them before performing MSA
tools to conform to the accuracy of results in rank to compare
them.
COBALT is used through default parameters, Gap
penalty (O/E): 11-1, End Gap Penalty (O/E): 5-1 RPS Blast:
ON, Constraint E-set a high ~ on: 0.03 and Conserved columns: ON.
Data sets taken from BAliBASE 2.0 and SABmark as refer-
ence data sets and either datum were used with COBALT
MSA Tool. As we discern that COBALT works for only pro-
tein order of succession format, DIRMBASE dataset, which is based
up~ nucleotide sequence, cannot be used.
The PRANK web server interface allows uploading
existing FASTA and HSAML files and displaying them in each
alignment browser window. Data can have existence input as amino acid,
codon and DNA sequences. Uploaded given conditions should be in
FASTA format and could exist done by pasting or choosing in the same manner with
file. Default settings of the program require gap rate as (0,05),
crack length as (5), K as (2.0) in the place of DNA alignment and gap rate
because (0.01) and gap length in the same proportion that (2) for Protein alignment. In the
cases that advance takes time, server gives a intimation num-
ber or the URL application to get the results later. We be able to dis-
play the results in every alignment browser and download them
in separate alignment formats.
Performing DbClustal needs couple data; the first one
is the protein succession of interest and second one should have existence
the BLAST report of the identical protein sequence. As the Db-
Clustal needs protein sequence, standard protein BLAST
should be used. We BLAST the FASTA toothed of our sequence
(data sets belong to Cooperation of BLAST and ClustalW2
in DbClustal shape it more efficient than COBALT and
WebPRANK. 2.0 and SABmark, BAliBASE facts set can
not be used DIRMBASE for it includes nucleotide se-
quences) and download results like text file then submit the
DbClustal through entering our protein sequence and Blast decision.
The input file of DbClustal should comprehend only one sequence
each time. The output could have ~ing monitored then saved in
Clustal, GCG MSF, PHYLIP, NEXUS, NBRF/PIR, GDE or
FASTA formats.
To bear a comparison our three different MSA Tools being of the kind which soft-
ware SuiteMSA, which runs MSA Comparator was used.
Each given conditions were performed with SuiteMSA and Consistency
%, SP Score and TC Score are recorded.
Results
COBALT DbClustal WebPRANK
Consistency %
BAliBASE-box10 6,409 Row facts 7,469
BAliBASE-box22 14,977 Row facts 6,322
BAliBASE-box32 19,753 Row given conditions 13,444
SABmark 1 81,132 98,052 36,932
SABmark 2 36,257 42,733 21,134
* The authors contributed equally to this be.
SABmark 3 43,713 95,868 31,285
SABmark 4 14,394 80,588 28,46
SABmark 5 12,59 78,377 5,875
DIRMBASE 1 - - 2,186
DIRMBASE 2 - - 9,498
DIRMBASE 3 - - 1,478
DIRMBASE 4 - - 6,235
ProBali box001 45,255 63,898 95,351
ProBali box022 35,897 77,435 31,384
ProBali box034 78,738 84,603 69,807
ProBali box036 75,945 85,653 70,061
ProBali box046 29,053 87,576 26,523
ProBali box050 60,06 65,543 55,285
ProBali box054 46,636 59,812 41,096
ProBali box076 84,466 43,977 84,261
ProBali box133 60,938 41,767 61,242
ProBali box153 34,049 54,345 34,137
DNABali RV60 46,242
DNABali RV61 8,961
DNABali RV62 7,992
DNABali RV63 1,898
DNABali RV64 4,158
DNABali RV65 45,093
DNABali RV66 9,918
DNABali RV67 5,655
DNABali RV70 3,568
DNABali RV80 8,119
Table 1: correspondence (%) of data taken from BAliBASE, DIRMBASE, SAB-
token, ProteinBali and DNABali which are performed through suiteMSA accord-
ing to results of COBALT, DbClustal and WebPRANK MSA tools.
Default setting of Decreasing setting
of
Increasing setting
of
box001 95,351 box001 21,829 box001 34,718
box022 31,384 box022 11,776 box022 26,217
box034 69,807 box034 46,977 box034 61,157
RV60 46,242 RV60 45,678 RV60 40,366
RV61 8,961 RV61 7,896 RV61 7,233
RV62 7,992 RV62 7,142 RV62 6,594
Table 2: agreement (%) of data taken from ProteinBali and DNABali
what one. are performed by suiteMSA according to results of changing break rate
and gap length value of WebPRANK MSA tool.
Figure 1: agreement of datasets performed in different MSA tools.
Figure 2: compatibility of datasets performed in different MSA tools.
Dbclustal has higher consistency, COBALT and WEBprank
showed parallel compatibility results. DbClustal didn’t work
with a view to the balibase 2.0 dataset directly to row output which is caused
by higher match on reference sequence by the result. And
COBALT has higher correspondence than WEBprank as the
figure1,. However, the dataset were not plenty to see
differences in detail. Drimbase dataset is formed by
nucleotide datasets with dashes and conversion of dataset to
protein sequences causes eradication of regions on sequence
order and intention. COBALT and DbClustal are specific
tools by reason of protein sequence but WebPRANK can labor for
both dataset types. As in that place is no other results for
simile we couldn’t say that WebPRANK has enough
consistence and reliability for this dataset.
ProteinBali facts set shows that Dbclustal has higher
compatibility due to addition of BLAST intelligence. Average
of consistency of DNABali is disgrace than other protein based
datasets. We concluded that protein based facts sets are more
efficient way to align than aligning nucleotide based data
sets. Except for RV60 and RV65, completely datasets shows lower
consistency which income inefficient aligning; in figure 2
* The authors contributed equally to this work.
As shown in table 2, we tried to make different multiple alignment
tool parameters. When we become greater/decrease gap rate and gap
continuance parameters of WEBprank, consistency is decreasing
because of both ways. changing gap rate causes the deviation of
algorithm optimization.
Discussion
Different MSA tools employment different data sets as input
some of them use datasets based ~ward nucleotide sequence and
perform with facts sets based on protein amino sour se-
quences. COBALT and DbClustal tools indigence input of amino
acid sequences in FASTA format at which place as WebPRANK is
able to use both amino acid and nucleotide sequences. Basi-
cally COBALT makes algebra and gives output depending
on the highest notch of possibility of sequences. When we
front at the consistency of COBALT comparing it to other
MSA tools, we could observe that data set of BAliBASE is greater amount of
efficient than others also for data set of SABmark consisten-
cy is further comparing to WebPRANK. Consistency of Db-
Clustal MSA tool as being SABmark data set is more than
COBALT and WebPRANK MSA tools. DbClustal uses
BLAST inquiry results so it gives a further trusting alignment.
Also this situation could attempt a row output error, which
resource the BLAST result gives 100% trial with target se-
quence so tool cannot align them for the re~on that it seen in BAliBASE re-
sults. As in mentioned COBALT and DbClustal could not
sustain a part any data from DIRMBASE because it based put ~ nu-
cleotide sequences. When we try to reverse nucleotide se-
quence to amino pricking sequence, converter programs automat-
ically set in or delete dashes, which are mis-placed and this
causes problem on SuiteMSA software. To perform SuiteM-
SA tool the two reference sequence and query sequence mouldiness
have the same length and identifier.
The WebPRANK server includes phylogeny-convinced
MSA, screening and post-processing in each easy understand-
able web interface. It widens the user base of phy-
logeny-persuaded multiple sequence alignment and allows the
execution of all alignment-related activity during the term of small se-
quence analysis projects using singly a standard web browser.
The data can be input as amino sharp, codon and DNA se-
quences and the program automatically detects their aggregate of characteristic qualities.
DNA sequences can be aligned using further complex models.
Protein-coding DNA sequences can be translated to
proteins/codons and in consequence back translated to DNA and gives
determination. When we look at the sum results of SuiteMSA,
WebPRANK consistency is exceedingly low. This tool is known to
have existence more suitable for small sequences [14] still the sequences
of our reference facts are long which can be the rational faculty of un-
satisfying scores.
It seems that cooperation of BLAST and ClustalW2
in DbClustal travel over it more efficient than COBALT and
WebPRANK. Also differences betwixt tools results decreas-
es as the sequences long duration increase. But it won’t exist appropri-
ate to make a existing conclusion about accuracy and preci-
sion of using tools as the scores could be problematic.
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* The authors contributed equally to this drudge.
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