HAlign statistics

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HAlign specifications

Information


Unique identifier OMICS_07879
Name HAlign
Alternative name HAlign-II
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Quan Zou

Information


Unique identifier OMICS_07879
Name HAlign
Alternative name HAlign-II
Interface Web user interface
Restrictions to use None
Input format FASTA
Programming languages Java
Parallelization MapReduce
Stability Stable
Maintained Yes

Maintainer


  • person_outline Quan Zou

Publications for HAlign

HAlign citations

 (5)
library_books

TopicalPdb: A database of topically delivered peptides

2018
PLoS One
PMCID: 5809007
PMID: 29432422
DOI: 10.1371/journal.pone.0190134

[…] y to be administered topically present within their proteins. The server searches such peptides and maps them on query protein submitted by the user. Multiple sequence alignment was implemented using HAlign[]. HAlign employs parallel computing and center star strategy for fast and efficient alignment. Structural alignment was implemented using MUSCLE[]. These alignment modules allow the users to a […]

library_books

Reconstructing evolutionary trees in parallel for massive sequences

2017
BMC Syst Biol
PMCID: 5751538
PMID: 29297337
DOI: 10.1186/s12918-017-0476-3

[…] handle the smallest dataset. So we only compare the performance with RAxML, Phangorn, STELLS and IQ-Tree []. All these three software tools need the aligned files as the input. So we firstly emloyed HAlign [] for multiple sequence alignment before the evolutionary trees reconstruction.The running time was compared and showed in Fig. . The initial human mitochondrial genomes dataset is about 10 MB […]

library_books

Partially local three way alignments and the sequence signatures of mitochondrial genome rearrangements

2017
PMCID: 5569537
PMID: 28852417
DOI: 10.1186/s13015-017-0113-0

[…] act alignments are only possible for a small number of sequences of short length. Therefore, heuristics and approximation methods have been applied in tools such as MAFFT [], CLUSTAL [], PASTA [] and HAlign []. Furthermore parallel computing has been introduced to reduce the actual running time for large scale alignments []. In our study, however, since we align only the three sequences for the sm […]

library_books

Accurate Identification of Cancerlectins through Hybrid Machine Learning Technology

2016
Int J Genomics
PMCID: 4961832
PMID: 27478823
DOI: 10.1155/2016/7604641

[…] h novel combinatorial machine learning strategy that can improve prediction accuracy.Machine learning techniques instead of traditional sequence alignment methods, such as PSI-BLAST [], HMMER [], and HAlign [], are often used to identify special proteins. Among these identification techniques, a support vector machine is the most common classifier used in computational proteomics, which involves v […]

library_books

Human Protein Subcellular Localization with Integrated Source and Multi label Ensemble Classifier

2016
Sci Rep
PMCID: 4914962
PMID: 27323846
DOI: 10.1038/srep28087

[…] the invariance. PSSM matrix represents the comparison results between the input protein sequence and its homologous protein sequence in Swiss-Prot database. The multiple sequence alignment tools are HAlign and PSI-BLAST (position-specific initiated BLAST). Each input protein sequence generates a PSSM matrix after multiple sequence alignment. The elements in PSSM matrix characterize homology level […]

Citations

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HAlign institution(s)
School of Computer Science and Technology, Tianjin University, Tianjin, China; Guangdong Province Key Laboratory of Popular High Performance Computers, Shenzhen University, Shenzhen, China

HAlign reviews

 (2)
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Quan Zou's avatar image No country

Quan Zou

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Desktop
The new URL is http://lab.malab.cn/soft/halign/index.html.

Web servers have been developed by the authors.
Anonymous user #1683's avatar image No country

Anonymous user #1683

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Desktop
A good tool on Hadoop platform