MaxAlign pipeline

MaxAlign specifications

Information


Unique identifier OMICS_15755
Name MaxAlign
Interface Web user interface
Restrictions to use None
Input format FASTA
Output format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Rodrigo Gouveia-Oliveira <>

Information


Unique identifier OMICS_15755
Name MaxAlign
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Output format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rodrigo Gouveia-Oliveira <>

Publication for MaxAlign

MaxAlign IN pipelines

 (3)
2012
PMCID: 3478181
PMID: 23057711
DOI: 10.1186/1471-2105-13-263

[…] homologous sequences are retrieved. secondly, the homologous sequences are aligned via the mafft [47] method to build the family sequence alignment. thirdly, the alignment is then processed by maxalign [48] to diminish the number of gapped columns in the alignment. fourthly, the mutual information between each two sites is calculated by the equation (1) [22], which consists of the mutual […]

2012
PMCID: 3532072
PMID: 23244412
DOI: 10.1186/1756-0500-5-472

[…] a blast query [41,42] against the ncbi-nr database [43]. the homologs identified were made non-redundant at the 90% level using cd-hit [44]. the final alignment was generated using muscle [45] and maxalign [46]., amongst the set of 67 protein cases available from [12], proteins that contain a single domain that interacts with more than one other domain in the set are disregarded. we chose […]

2011
PMCID: 3111387
PMID: 21569384
DOI: 10.1186/1471-2148-11-123

[…] settings, were made for all sequences. the alignments and transmembrane predictions were viewed in jalview (v2.5.1) [41]. the alignments were edited to remove poorly aligned sequences, using the maxalign (v1.1) [29] exclude selection, with the additional goal to retain all human sequences and achieve aligning tm segments in >80% of the sequences for each conserved tm block. all editing […]

MaxAlign institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
MaxAlign funding source(s)
Supported by grant SFRH/BD/12448/2003 from the Foundation for Science and Technology from the Portuguese Ministry of Science.

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