For example if you are doing de novo transcriptomics. The result will be a series of individual contigs, each of which was aligned using the Clustal algorithm. You can group your sequences using the standard naming handles and send them one-at-a-time to the Clustal assembly engine. An overview of different problems and approaches is available on Wikipedia. Sequence assembly refers to the process of merging DNA fragments into larger 'contigs' for subsequent analysis. Depending on the experimental goal and on what sort of sequencing you were doing e.g DNA-seq or RNA-seq you may or may not encounter contigs.Ĭontigs are simply reads that have been assembled together. Using Clustal with Assemble by Name Assemble by Name using Clustal is also available. This site is dedicated to software for DNA sequence assembly and alignment. All reads are stored in a single fastq file per replicate, where all reads in that file are usually of uniform size e.g all 5 million reads are 100bp long.Īs a bioinformatician your first job is to identify where about those reads come from. If your input data is paired, you can use Contig>Order Contigs to automatically create scaffolds based on the paired data. From a single run (it will really depends on the run) you can get millions of reads, where each read will be set bp size e.g 100bp long. There are several options for organizing contigs in an assembly. Right now MySeq produces reads anywhere between 50-150 base pairs long (bp). The Assemble by Name tool allows you to choose a portion of the fragment name to act as a shared identifier, or 'assembly handle. Usually sequenced reads refer to somewhat digital information obtained from the sequencing machine (for example Illumina MySeq) and stored in the fastq file with quality scores per base. Reads are just a short hand for sequenced reads. Both contigs and reads are DNA/RNA or aa sequences Sequence is a generic name describing order of biological letters (DNA/RNA or amino acids). My understanding of those three words as follows:
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