BIP-Align Downloads Details
Details on downloading BIP-Align input data:BIP-Align requires two types of input data - genomic DNA sequence and transcript mRNA/cDNA/EST data.
Genomic DNA data can be downloaded from any source. The only limitation is that the sequences must be in Fasta format, with one chromosome, contig or scaffold per fasta file. The name of the fasta file must also be the same as the sequence ID, i.e. the sequence for chr1 must be in chr1.fa
One source of genomic data is UCSC, genome downloads are available from http://hgdownload.cse.ucsc.edu/downloads.html
Transcript data can be in GenBank, UniGene, or dbEST format. If the user has a different data format, either the file can be preprocessed and split into separate flat files, or a new parser can be created for the format.
GenBank: The easiest way to obtain GenBank data is by an online Entrez query: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=nucleotide
To download all transcripts from a single organism, follow these steps:
- Select 'Nucleotide' in the Search drop-down box.
- In the next box (after 'for') type the organism's name, a space, then [orgn]
- Click the 'Limits' tab
- Select mRNA from the Molecule drop-down box
- Add any additional liit criteria you would like to use. Your screen should look something like this:
6. Click the 'GO' button7. In the Display drop-down, select GenBank 8. In the send to drop-down, select File
A Save file dialog will appear. Select a location and filename, and the download will begin.
Downloading dbEST data:
dbEST data can be downloaded as daily reports by anonymous FTP from ftp://ftp.ncbi.nih.gov/repository/dbEST/
The data for your organism must be separated from these reports, as they are multi-organism files
Downloading UniGene data: UniGene data can be downloaded from ftp://ftp.ncbi.nih.gov/repository/UniGene/
You must select the .seq.uniq, .lib.info and .data files for your organism.
Back to TOP
For any comments or suggestions, send an e-mail at: BIP_FEEDBACK@asu.edu
