Genome Visualization Tools:
- UCSC Genome Browser
- popular, free genomic visualization tool for a wide variety of organisms
- also serves as a database for genomic sequences and features
- Integrative Genomics Viewer (IGV)
- very efficient tool for visualizing almost any type of genomic data
- open-source
- Gbrowse - open-source genome browser
Sequence Alignment:
- BLAST - search for similar DNA sequences in GenBank
- ClustalW - multi-species genome alignment
- TCoffee - multi-species genome alignment
- Mauve - multi-species alignment and visualization tool to detect segments of conserved sequence
General DNA-Seq Tools:
- samtools
- popular, free tool to extract data from .SAM alignment files
- Picard - java-based version of samtools
- see short read aligners necessary for upstream analysis
- Galaxy
- open-source, cloud-based suite of popular sequence analysis tools (including deep sequencing analysis
- GATK
- toolkit for analysis of next-generation sequencing data
- previously open-source, but now requires a commercial license
- CLC Bio Genomics Workbench
- commercial software covering a wide variety of applications such as sequence alignment, SNP/DIP detection, de novo assembly, etc.
- CLC Bio Genomics Workbench also has the functionality of CLC Bio Main Workbench for standard sequencing analysis (cloning, primer design, etc.)
- both are commercial programs that require a purchased license
- Nexus Copy Number
- commercial software for analysis of copy number alterations
- works for a variety of microarray platforms as well as for deep sequencing analysis
- SeqAnswers Software List
Transcription Factor Motif Analysis:
- TRANSFAC
- database of transcription factor motifs
- a subscription is required to access the most recent annotations, but older versions are freely available
- A plug-in is available within CLC Bio (a commercial program for genomics analysis)
- JASPAR
- free database of transcription factor motif sequences
- TFsitescan
- free tool to search for transcription factor motifs
- MEME Suite
- tools for ab initio motif finding
- rVista / VISTA Suite
- tool for searching motifs conserved across closely related organisms
- TESS
- transcription factor search system
- unfortunately, this tool now has to be run locally
Mutation Analysis:
- VarScan
- open-source variant calling tool
- see short read aligners necessary for upstream analysis
- usually also requires something like samtools to create input file
- SeattleSNPs Genome Variation Server
- tool to filter candidate variants (based upon frequency, predicted function, etc.)
- ANNOVAR (pronounced Anno-Var)
- tool to filter candidate variants (based upon frequency, predicted function, etc.)
- wANNOVAR is the web-based interface
- GWAS Catalog
- NHGRI database of SNP-based phenotypic / disease associations
- Promethease
- open-source tool for personalized genomic analysis
- it is technically free to use, but you can pay $5 to get your report more quickly
- uses annotations from SNPedia
- Interpretome
- Genome interpretation tool similar to Promethease
- In my opinion, nicer interface. However, it currently only works with raw data from 23andMe and Lumigenix.
- SNPedia
- crowd sourced annotation of SNP associations
- includes some publicly available genomes
- List of tools from the Swiss Institute of Bioinformatics
- MAT peak calling algorithm
- There is an open-source implementation as well as a GUI-based implementation in various programs (likePartek Genomics Suite, a commercial program)
de novo Assembly Algorithms:
Other Tools:
- Primer3 - PCR primer design
- Repeatmasker - identifies repetitive elements within a DNA sequence
- Webcutter - detects restriction enzyme sites in a DNA sequence
- Translate - a tool that allows translation of nucleotide (DNA / RNA) sequence into a protein sequence
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