Current Protocols in Bioinformatics - Sample Data

The files below accompany the units in Current Protocols in Bioinformatics. They can be used to replicate the detailed examples presented in the protocols.

To download a file, right-click on the file name, and select "save as" to save to your computer.

Unit 1.11: TAIR
Basic Protocol 4
Download: WRKYFamily.txt (Text: 0.85 KB)
A list of 82 AGI locus identifiers for Arabidopsis all belonging to the WRKY transcription factor family

Basic Protocol 9
Download: ExpressionSample.txt (Text: 20.95 KB)
Arabidopsis expression dataset for low temperature regulatory circuits, taken from the functional genomics expression project http://arabidopsis.org/info/expression/index.html

Unit 2.3: ClustalW and ClustalX
Basic Protocol
Download: 1wit.tfa (Text: 0.54 KB)
FASTA file of five unaligned immunoglobulin superfamily domains

Alternate Protocol
Download: 1tlk.aln (Text: 1.12 KB)
Clustal alignment of the C-2 type subfamily

Download: 1wit.aln (Text: 1.06 KB)
Clustal alignment of five immunoglobulin superfamily sequences with the secondary structure assignments

Unit 3.13: FrameSearch
Basic Protocols 1 & 2, Alternate Protocols 1 & 2
Download: BA000007.aa (Text: 2.09 MB)
Amino acid translations of all putative genes found in this bacterial genome by the lab where it was sequenced, as a single FASTA format text file

Download: BA000007.fna (Text: 5.58 MB)
Nucleotide sequence of all putative genes found in this bacterial genome by the laboratory where it was sequenced, as a single FASTA format text file

Unit 3.3: BLAST
Basic Protocol
Download: NM_000558.3 (MS Word: 19.46 KB)
FASTA file of the mRNA for human hemoglobin a1 (GenBank Id.: NM_000558.3)

Unit 4.13: MZEF
Basic Protocols 1 & 2, Alternate Protocol
Download: M12523.fasta (Text: 19.63 KB)
FASTA file19-kb human genomic DNA sequence containing the serum albumin (GenBank Id: M12523)

Unit 4.3: geneid
Basic Protocol 1
Download: example1.fa (Text: 32.54 KB)
FASTA file of a 32-kb region of human chromosome 21

Basic Protocol 3
Download: example2.fa (Text: 47.80 KB)
FASTA file of a 47-kb region of human chromosome 22

Download: example2.evidences.gff (Text: 0.17 KB)
Annotated gene features of the example2.fa sequence

Download: example3.fa (Text: 32.54 KB)
FASTA file of a 32-kb region of human chromosome 15

Download: example3.EST1.gff (Text: 0.12 KB)
Annotated gene features of the example3.fa sequence

Download: example3.EST2.gff (Text: 0.08 KB)
Annotated gene features of the example3.fa sequence

Download: example3.EST3.gff (Text: 0.08 KB)
Annotated gene features of the example3.fa sequence

Download: example3.promoter.gff (Text: 0.04 KB)
Annotated gene features of the example3.fa sequence

Unit 5.7: Using VMD
Basic Protocols 9, 10, 11, 12, & 13
Download: 1fqy.pdb (Text: 158.11 KB)
pdb coordinate file for human aquaporin (Murata et al., 2000)

Basic Protocols 11, 12, & 13
Download: 1lda.pdb (Text: 203.15 KB)
pdb coordinate file for E. coli GlpF (Tajkhorshid et al., 2002)

Basic Protocols 1, 2, 5, 6, 7, & 8
Download: 1ubq.pdb (Text: 50.90 KB)
pdb coordinate file for ubiquitin (Vijay-Kumar et al., 1987)

Basic Protocols 14, 15, & 16
Download: distance.tcl (Text: 1.58 KB)
An example tcl script

Basic Protocols 3, 4, 14, 15, & 16
Download: pulling.dcd (Text: 31.43 MB)
dcd molecular dynamics trajectory file of a protein-pulling simulation

Basic Protocols 3, 4, 14, 15, & 16
Download: ubiquitin.psf (Text: 2.73 MB)
psf structure file for ubiquitin that defines connectivity of atoms

Basic Protocols 11, 12, & 13
Download: 1j4n.pdb (Text: 206.06 KB)
pdb coordinate file for bovine aquaporin (Sui et al., 2001)

Basic Protocols 9, 10, 11, 12, & 13
Download: 1rc2.pdb (Text: 127.97 KB)
pdb coordinate file for E. coli aquaporin (Savage et al., 2003)

Basic Protocols 5, 6, 7 & 8
Download: beta.tcl (Text: 0.14 KB)
An example tcl script

Basic Protocols 14, 15, & 16
Download: equilibration.dcd (Text: 19.49 MB)
dcd molecular dynamics trajectory file of an equilibration simulation

Basic Protocols 11, 12, & 13
Download: spinach_aqp.fasta (Text: 0.27 KB)
An example fasta protein sequence file

Unit 6.2: TreeView
Basic Protocol 1
Download: NewickTree.tre (Text: 0.36 KB)
Sample Newick file

Unit 9.2: SQL
Alternate Protocol 1
Download: oligo.txt (Text: 0.30 KB)
Tab-delimited trial data file for batch method loading of data into table