Sequence assembly

From MyBio

Contents 1 Categories which link here 2 Related subcategories 3 Sequence assembly - Quick Links 4 Sequence assembly - Web Resources 4.1 Locally installed sequence assembly software

[edit] Categories which link here

• Sequence manipulation
• Sequences

[edit] Related subcategories

• Gene synthesis (incorporating Design of Synthetic Genes)

[edit] Sequence assembly - Quick Links

MIRA genome and EST assembler		Merger
CAP3 Tigem		ESSEM
Transcript Assembly Program		Phrap, Consed
MIRA 2		DNA Baser - commercial sequence assembly program
GSC - FASSI		AMOS

[edit] Sequence assembly - Web Resources

MIRA genome and EST assembler Whole Genome Shotgun and EST Sequence Assembler. MIRA2 system is the successor of MIRA with new algorithms, and improved reliability and execution speed. Labs find MIRA2 useful for assembly of extremely 'unfriendly' projects containing lots of repetitive sequences. The miraEST module is suited for assembly of non-normalised EST projects and for detecting SNPs.

Merger Merge two overlapping nucleic acid sequences.

CAP3 Tigem Contig Assembly Program Based on Sensitive Detection of Fragment Overlaps. Third generation of the CAP sequence assembly program. Includes a number of improvements and new features including the capability to clip 5-primer and 3-primer low-quality regions of reads, the use of base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints.

DPL Forum: Too few categories!

ESSEM Est aSSEmbly tool using Malig. Computational tools for the study of DNA sequence assembly powered by sequential, distributed and massive parallel machines. Graphical interface that allows the fast identification of the alignments, the results and the status of your query are sent by e-mail. On-line sequential web application is accessible. Allows the reconstruction of DNA sequences from a set of fragments. The fragments are inputted in FASTA format. The application takes these fragments and tries to infer the parental DNA sequence.

DNA Baser DNA Baser is an easy to use software package providing DNA sequence assembly functions (simple and batch), contig editing functions and chromatogram viewer/editor. We have created a fast assembly engine and a range of features that greatly speed up the process of sequence assembly and mutation analysis. It provides automated end trimming (clipping), so there is no need to trim manually the low quality bases from the ends of the trace files before contig assembly. This saves considerable time, especially when assembling many DNA sequences. DNA BASER offers a smart navigation system that takes you to the location of each sequence ambiguity / mutation with only a single click. Our proprietary sequencing error correction algorithm provides further timesaving. The truly user-friendly interface makes DNA Baser the best choice for DNA contig assembly. For more details, see the DNA BASER Features page. 60 day full working trial!

Transcript Assembly Program TAP and FAST TAP. Transcript Assembly Program is an EST-based gene finder that infers the predominant and alternative gene structures in anonymous genomic sequences. The entire prediction process consists of 3 steps. (1) The genomic sequence is searched against dbEST using WU2BLASTN (Gish, 1996-2001). (2) High-scoring EST hits are aligned to the genomic sequence using sim4 (Florea et al. 1998). (3) Based on genomic EST alignments, TAP predicts the predominant gene structure on both strands of the genomic sequence, identifies the poly-A sites and gene boundaries, and infer alternatively spliced gene structures. The program was developed mainly for predicting human genes, but is also applicable to other species.

Phrap, Consed Sequence assembly tools which have been used on very large assemblies of around 200,000 reads. Consed is used at over 2000 sites, actively used in 36 countries in biotech, pharma

MIRA 2 Whole Genome Shotgun and EST Sequence Assembler. The MIRA2 system is the successor of MIRA. Additional years of knowledge and experience were incorporated, new algorithms devised, reliability and execution speed improved. Labs find mira2 useful for assembly of extremely unfriendly projects containing lots of repetitive sequences. The miraEST module is suited for assembly of non-normalised EST projects and for detecting single nucleotide polymorphisms (SNP) in the transcriptome sequences. The MIRA2 assembler is currently only available for Linux system.

GSC - FASSI FASSI is a stand-alone application that calculates BAC end and BAC overlap length constraints from clone fingerprint map contigs created by the FPC package.

[edit] Locally installed sequence assembly software

AMOS consortium is committed to the development of "A Modular, Open-Source (AMOS) whole genome assembler" for linux. Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure.