MutExt

A  fast^*) nucleotide sequence alignment program, with customizable output and batch processing capabilities.

The help file is not finished yet but you can download  MutExt 1.0.6 32 bit (Windows XP/SP3, Vista or 7) here (SetupMutExt_1_0_6.exe   519,521 bytes   2011-10-19).

The GUI was written in VB.Net and compiled for the .Net framework 3.5 (part of Windows since WinXP SP3).

• 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 Features

• Global (Needleman-Wunsch) or local (Smith-Waterman) 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 phylogenetic analysis)
• 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)

Older Versions

MutExt 1.0.4 32 bit (Windows XP/SP3, Vista or 7   518,687 bytes)

MutExt 1.0.2 32 bit (Windows XP/SP3, Vista or 7, SetupMutExt.exe 510,754 bytes)

The GUI was written in VB.Net and compiled for the .Net framework 2.0 (part of Windows since WinXP SP3).

With updated installer because the version 1.0 of the installer didn't included code for the UAC (user access control) of Windows Vista and 7. This was corrected as well as writing the correct path of the reference sequences in the applications ini file.