A fast*) nucleotide sequence alignment program, with customizable output and batch processing capabilities.
* The alignment of 1000 HIV1 PR/RT sequences, average length of 1302bp, takes 6 to 25 seconds on a standard PC running at 2 GHz.
Time depending on alignment, sequence quality and output options.
- Global (Needleman-Wunsch) or
nucleotide sequence alignment
- Writes decorated alignment and mutations lists
- Loadable set of reference sequences (HIV-1, HBV and HCV provided as samples)
- Loadable set of subtype references (HIV-1 gag, PRRT and IN provided as samples)
- Automatic detection of best matching reference sequence
- Output of comprehensive csv files containing not only aa substitutions and indels but
additional information such as sequence crc, alignment score, subtype, base counts etc. and other optional fields
- Output of aligned sequences, with the option to skip determined positions (e.g. for subsequent
- Build consensus sequence
- Reads single or - in batch mode - multi sequence fastas, csv files or folders (directories)
- Breaks down multi sequence fasta files (or csv files), writing each sequence to it's own file
- Merge fastas in a folder, writing a single fasta or csv file
- Split a sequence at the location of a search pattern (fuzzy level adjustable)
- Complement and/or revert sequence
- Detection of base calling errors such as indels of one base
- Jump to error position in fasta file
- Sequence distance profiles: uses a special binary format to select most similar sequences to a query sequence, with "patient IDs" if present
- Customizable output using csv and css control files (e.g. to decorate scored mutations)
- Generates a list of customizable text, containing the filenames of sequences with errors
- Generates a set of fasta files for testing purposes, consisting of all combinations of mutations in a given set
You can download ▼ MutExt 1.5.1
(for Windows XP/SP3, Vista, 7; 32 or 64 bit) here.
The GUI was written in VB.Net and compiled for the .Net framework 3.5 which is part of Windows since WinXP SP3.
(File: SetupMutExt_1_5_1.exe Size: 692,078 bytes Date: 2015-11-20).
New in version 1.5.1: (Older versions here)
New in version 1.5:
- Corrected the bug in the test fastas generator w.r. to the 297 bases offset in HIV PR/RT sequences. The positions of RT mutations
in a joint fasta, with protease and reverse transcriptase, are now correct.
- Bugfix for empty path string
New in version 1.3.0:
- Added the function to generate a set of fastas files for testing purposes. The function is based on the "scored mutations" file
reading all entries with a format id=1 (see 'Scored mutations file' in MutExt Help). The corresponding mutations are offered as
check boxes and a full combination set of all checked mutations will be produced. Instead of using the 'official' scored mutations
file, you can provide any other one, as long as the format is the same. There is an option to include only one mutation per position (i.e. 41GS 56IM would
generate the four fastas with wild type; 41G; 56I; 41G 56I instead of 9 fastas with wild type; 41G; 56I; 41G 56I; 41S; 41S 56I; 56M; 41G 56M; 41S 56M).
- Increased the space in the subtypes list and added subtype profiles for HCV NS3, NS5A and NS5B (~70 genotypes/subtypes).
New in version 1.2.0:
- In the message log window there is a new Command tab. It is possible to generate a customizable list of strings (e.g. for a CMD-file), using the path and filename of sequences that were listed in the Batch-Log window, as containing errors. This could usefully be a list of commands (hence the name) like move or copy in combination with the filenames.
- Updated list of HCV scored mutations.
- Changed the order of columns in the CSV output file! Now scored mutations (SCMT) are placed before substitutions (SUBST),
making the file more readable.
- Just a little bugfix concerning the message log that was copied truncated to the clipboard.
- A new menu entry combining revert and complement sequence.
- Some new entries in the HIV1_HxB2_FULL.fas reference set.
Here is an actualized list of scored mutations for HCV: HCV_SCMT.csv. If interested, copy or merge this file to your version in the Profiles subfolder of the MutExt data folder (default Documents/MutExt_Data/Profiles).
New in version 1.1.0:
New in version 1.0.8:
- 'Scored mutations' are now considered even if they correspond to the 'wildtype' (The amino acid at a scored position is written in the mutation list even if there is no mutation in the strict sense. I.e. if the file xxx_SCMT.csv contains the line PR;26;1;Y and the reference at position 26 is Y, the output will be Y26Y instead of nothing.
- There is a new option to discard one-base-insertions in the alignment. This doesn't alter the fasta nor the raw alignment, but in the corrected alignment and in the mutation list, the insertion is ignored. Warnings in the message log are not suppressed by this option.
New in version 1.0.7:
- Only changed compile options to target CPU x86 so that the program runs now on 64 bit Versions of Windows as well.
New in version 1.0.6:
- Bug fix to handle empty or only '-' containing sequences
New in version 1.0.4:
- Optional output of silent mutations in batch mode.
- Additional CSV file with number of mutations and silent mutations per site (batch mode).
- Handles sequences up to 9996 bases.
- 2011-10-10: corrected a bug in the part that handles ambiguity codes to calculate consensus sequences.
- Display consensus base in the table of proportions per site.
- New function to create consensus sequences out of a set of aligned sequences, with or without
ambiguity codes in the resulting consensus (adjustable thresholds).
In the CSV files produced in batch mode, there is an additional column "QA Problems" which contains the
error messages from the message log.
- The weight of the gap open and extend penalties were altered in the local alignment procedure. Alignment results are
now more similar to global alignment when the same gap open and extend penalties (e.g. 10 and 4) are used.
MutExt 1.0.6 32 bit (Windows XP/SP3, Vista, 7 519,521 bytes)
The GUI for 1.06 was compiled for the .Net framework 2.0 (part of Windows since WinXP SP3).
© 2009-2017 Eugen Schülter