MultiScan – Motif Scan in Multiple Alignments with Background built from HtBackground

MultiScan

:: DESCRIPTION

MultiScan: Multiple species motif scanning with heterogeneous background constructed by HtBackground.

::DEVELOPER

Qing Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MultiScan

:: MORE INFORMATION

Citation

Chen, G. and Zhou, Q.
Heterogeneity in DNA Multiple Alignments: Modeling, Inference, and Applications in motif finding.
Biometrics, 66: 694-704.

MAPSCI 1.0 – Multiple Alignment of Protein Structures and Consensus Identification

MAPSCI 1.0

:: DESCRIPTION

MAPSCI is an algorithm to compute a multiple structure alignment for a set of proteins and to generate a consensus structure.

::DEVELOPER

MAPSCI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C++ Compiler

:: DOWNLOAD

 MAPSCI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Feb 2;11:71. doi: 10.1186/1471-2105-11-71.
Multiple structure alignment and consensus identification for proteins.
Ilinkin I1, Ye J, Janardan R.

MACSE 2.05 – Multiple Alignment of Coding SEquences

MACSE 2.05

:: DESCRIPTION

MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

::DEVELOPER

MACSE team

:: SCREENSHOTS

MACSE

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 MACSE

:: MORE INFORMATION

Citation

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel JP Douzery
PLoS One 2011, 6(9): e22594.

MAFFT 7.487 – Multiple Alignment Program

MAFFT 7.487

:: DESCRIPTION

MAFFT (Multiple sequence Alignment based on Fast Fourier Transform)is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc.

MAFFT Server

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux

:: DOWNLOAD

MAFFT

:: MORE INFORMATION

Citation

Katoh, Rozewicki, Yamada 2019
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Briefings in Bioinformatics 20:1160-1166

Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees.
Yamada KD, Tomii K, Katoh K.
Bioinformatics. 2016 Jul 4. pii: btw412

Kazutaka Katoh and Hiroyuki Toh
Parallelization of the MAFFT multiple sequence alignment program
Bioinformatics (2010) 26 (15): 1899-1900

blast2malign 0.3 – Create Multiple Alignment from the database hits of a BLAST search

blast2malign 0.3

:: DESCRIPTION

blast2malign is an easy to use script that creates a multiple alignment (relative to the query) from the database hits of a BLAST search. Multiple HSPs from a database sequence are combined or separated depending on their relationship to each other.

::DEVELOPER

Danny Rice

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 blast2malign

:: MORE INFORMATION

multiAlignFree 1.0 – Multiple Alignment-Free Sequence Comparison

multiAlignFree 1.0

:: DESCRIPTION

multiAlignFree is an R package which intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

 multiAlignFree

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2690-8. doi: 10.1093/bioinformatics/btt462. Epub 2013 Aug 29.
Multiple alignment-free sequence comparison.
Ren J1, Song K, Sun F, Deng M, Reinert G.

MASTR 1.0 – Multiple Alignment of STructural RNAs

MASTR 1.0

:: DESCRIPTION

MASTR performs multiple alignment and secondary structure prediction on a set of structural RNA sequences.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MASTR

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Dec 15;23(24):3304-11. Epub 2007 Nov 15.
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
Lindgreen S, Gardner PP, Krogh A.

RMfam 0.3 – Multiple Alignments and Probabilistic Models of RNA Motifs

RMfam 0.3

:: DESCRIPTION

RMfam is a database of annotated multiple sequence alignments and probabilistic models for a number of RNA motifs.

::DEVELOPER

Gardner Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RMfam

:: MORE INFORMATION

Citation

Annotating RNA motifs in sequences and alignments.
Gardner PP, Eldai H.
Nucleic Acids Res. 2015 Jan;43(2):691-8. doi: 10.1093/nar/gku1327

PROBCONS 1.12 – Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

PROBCONS 1.12

:: DESCRIPTION

PROBCONS is an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PROBCONS

:: MORE INFORMATION

Citation

Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005.
PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment.
Genome Research 15: 330-340.