Sequence Analysis Tools for Molecular Biologists

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Trimming Vector Sequences Using cross_match

Many raw sequences from automated sequencing machines contain vector sequences at the beginning and/or end. MacVector Assembler lets you mask these out using the cross_match algorithm. To use this you just need to supply the sequences of the vector(s) you used for the cloning - there is no need to indicate the cloning site you used as cross_match can easily identify the exact position where the vector sequences terminate. Like phred, the cross_match executable is a Universal Binary and MacVector Assembler splits up jobs between multiple CPUs if they are available. After processing by cross_match, you can view the masked vector sequences in the trace editor window where they appear in grayed out italics.


A trace editor window after


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Creating a Sequencing Project

Base Calling Using phred

Vector Trimming with cross_match

Assembling Sequences using phrap

Editing and Analysis of Contigs

NGS Reference Assembly using Bowtie

NGS de novo Assembly using Velvet

Comparing Assembler and AssemblyLIgn

SplitFastqFile - a ultility to break up large fastq files.

Functional comparison with Sequencher