Programs List   

Workflow Diagrams:   

Annotation to user supplied gDNA sequence Annotation to Genome Browser latest freeze SNPs Data Collector SNP Genotyping Assay Designer Accessory Tools

Annotation to user supplied gDNA sequence

By supplying both source data and gDNA data, you can get the annotation results

SNP mapping SNPs + gDNA in FASTA -> annotation

Annotate SNPs onto gDNA

BLAST/BLAT-based approach

Primer mapping

 primers + gDNA in FASTA -> annotation

Annotate primers onto gDNA
General fragments in FASTA for annotation source data in FASTA + gDNA in FASTA -> annotation

Annotate fragments onto gDNA
General fragments in table for annotation source data in tabular text + gDNA in FASTA -> annotation

Annotate fragments onto gDNA
STS mapping <STS list +>  gDNA in FASTA -> annotation

e-PCR based STS mapping

 e-PCR-based

Exon defining (BLAT)

 cDNA in FASTA + gDNA in FASTA -> annotation

Annotate exons onto gDNA

 BLAT-based

Exon defining (Sim4)

 cDNA in FASTA + gDNA in FASTA -> annotation

Annotate exons onto gDNA

 Sim4-based
Repeat element mapping gDNA in FASTA -> annotation

Annotate repeat elements onto gDNA

 RepeatMasker-based

Annotation migration

 Annotated gDNA in Genbank + target gDNA in FASTA -> annotation

Migrate annotation from one gDNA to another

  

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Annotation to Genome Browser Latest Freeze (Attention: Human genome sequence only!)

By supplying only annotation source data, annotation can be made on the latest public assembly gDNA sequences.  Results can be viewed on Genome Browser by uploading file produced by this program as a "custom track" to Genome Browser

SNP mapping SNPs  -> annotation

Annotate SNPs onto Genome Browser's latest freeze

 BLAT/BLAST-based
General fragments in FASTA for annotation source data in FASTA + gDNA in FASTA -> annotation

Annotate fragments onto Genome Browser's latest freeze

Primer mapping

 primers  -> annotation

Annotate primers onto Genome Browser's latest freeze

 BLAST-based
Exon defining cDNA in FASTA  -> annotation

Annotate exons onto Genome Browser's latest freeze

 BLAT-based

Annotation migration

 Annotated gDNA in Genbank -> annotation

Migrate annotation to Genome Browser's latest freeze

  

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SNP Data Collector

Allele frequency finder  rs SNP IDs list -> SNP allele frequency data from multiple databases Allele Frequency
SNPSequer rs SNP IDs list or DNannotator format SNP data -> SNPs with defined length flanking sequences in multiple formats for assay design Flanking Sequence
     

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SNP Genotyping Assay Designer

SNP Cutter  rs SNP IDs list or SNP data -> genotyping assay primers, fragments size etc. PCR-RFLP assay
Primer Nerd SNP data (FASTA format) -> genotyping assay primers FP assay
     

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Utilities for data processing

Clean FASTA sequence

 FASTA sequence -> cleaned one

remove extra white spaces and undesired symbols from FASTA seq

 BLAST service
Remove batch data from FASTA file FASTA sequence + list of ID -> FASTA seq without entries in the list

Remove a set of sequence from a FASTA format sequence collection

Create unique BLAST query data set

 FASTA sequence -> FASTA seq without duplicated entries

remove duplicated FASTA sequences from the query data file

1 to 1 BLAST

 one FASTA vs. one FASTA

one sequence against another

Many to many BLAST

 multiple FASTA vs. multipleFASTA

many sequences against many others

Many to NCBI db BLAST

 multiple FASTA vs. NCBI databases

many sequences against online database

BLAST results parsing & filtering

 BLAST results -> filters tabular text

    parse & filter BLAST results according to matched length and percentage
 

Convert Mac format to Unix format

 If you primarily using Mac to prepare your data file, you will have to use this function to reformat data before doing other DNannotator analysis. for Mac user
 
 

Batch cDNA align to 1 gDNA (Sim4)

 many cDNA aligned to gDNA Sim4
 

Create Genbank format feature header

 FASTA format -> Genbank format with gb-header

format Genbank format header, so that it can be used to collect annotation from DNannotator

 gb-header manipulation (after cleanup,  individual or combined gb-header files can be  viewed by Artemis)
Extract gb-header from Genbank Genbank format -> gb-header

obtain gb-header from a complete Genbank format data file, so that annotation procedure can be more compact
Merge multiple gb-header files multiple gb-header -> one gb-header

combine multiple gb-header files (for one gDNA sequence.)
Cleanup gb-header file  

remove duplicated annotation, and sort the features
Merge gb-header with sequence data gb-header + FASTA sequence body -> complete Genbank

return a complete Genbank format data
Conversion between standard Genbank format gb-header and VNTI format gb-header Standard Genbank <-> VNTI Genbank

since DNannotator provide both standard and Vector NTI format feature data, here you have the 2nd chance to switch your choice (>10 Mb sequence better with Artemis)
 

Extract features table from Genbank data file

 Genbank -> Features table

get feature table from standard Genbank files

 Feature table manipulation

Format/create Genbank format sequence body

 Sequence -> Genbank sequence body

format sequenced body, so that it can be combined with Genbank format feature head

Merge DNannotator feature table

Multiple features table -> one combined features table

use command:

in Unix: cat [file1] [file2] > [combined_file]

in DOS: type [file1] [file2] > [combined_file]
Extract feature-related sequence FASTA sequence + Feature table -> feature sequence

Use feature table to fetch feature-related sequence fragments
Convert Genbank format into GFF Retired my own web application, please use D.G. Gilbert's original Readseq instead:

http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi

Convert DNannotator feature table into GFF

 DNannotator Feature table -> GFF

Slight change makes DNannotator feature table comply with GFF standard
     
Primer Evaluation (currently convert primer list into FASTA format, so that it can be used for database searching)  
Screen primer for repeats primers -> primers within repeats

Find out primers located in repeats (including Alu, MER, LINE, RNA, SINE, LTR, simple repeat)

 For duplications
Remove features from gb-header or feature table gb-header/features table + list of features -> gb-header/features table without the features

Remove annotations/features from a gb-header (Genbank format data) or/and a feature table according to a list

Search for duplicates gb-header/features table -> duplicated annotations

Search a gb-header (Genbank format data) or a feature table, to find all duplicated elements and their duplication times
     

Compare two lists

 List 1 + list 2 -> Unique entries, duplicated entries, and overlapped entries Data manipulation

Extract subset data

Master data + keyword list -> output subset data including or excluding rows with keywords

Merge two tables

 Table 1 + table 2 -> merged table according to shared index data
     

Remove HTML tags

 HTML format file -> plain text file

Create plain text file from HTML file

  
Annotation to user supplied gDNA sequence Annotation to Genome Browser latest freeze SNPs Data Collector SNP Genotyping Assay Designer Accessory Tools

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Bug Report

11/12/2003 updated