Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Page Count: approx. 2,600
Print ISSN: 1934-3396
Online ISSN: 1934-340X

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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 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