CBU - Computational Biology Unit

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Warning: the scientific code of this tools is currently not supported: errors may occur

Cross-Hybridization - realtime search
Pre-processed search

Please enter FASTA sequence(s):

Or accession entries (e.g. BG062929):

Or enter the name of a file containing query sequence(s)

Or enter the name of a file containing query accession id's(s)

Search for:
Output formatting:


Required percentage (type A)
Required length of type A window (def. 50)
Required length (type B)
Maximum overall percentage identity (def. 100%)
Use similarity relative to query length
Na+ concentration (in molar), for Tm calculations M
Size of gc-clamp (in #bp, def. 10)


Number of output alignments:
Gap opening:
Gap extension:
Word size:
Mismatch penalty (default -3):
Show hits above E-value:
Dust filter:
Gapped alignment:

Cross-hybridization tool

This tool is used by entering one or several nucleotide sequences, or just accession ids. The input sequences will be queried towards a specified database, UniGene unique is in general a good choice. Criteria for the two different similarity types can be changed:
  • Type A: More than X% sequence identity over a given length of sequence.
  • Type B: 100% similarity over shorter sub-sequences. Typical length thresholds for these sub-sequences vary from around 15bp and up.
In the user interface different options may be set:
  • CROSS-HYB SETTINGS. Here settings regarding what may be accepted as a (cross) hybridization is set.
  • BLAST-SETTINGS. Here the detailed settings for the underlying BLAST execution may be set.
  • In addition, one must choose database to use as "transcript pool", output formatting, and what to search for. Normally, use the Combined A and B search.

Problems? mail to [contact@bioinfo.no]

List of references:

Kristian Flikka, Fekadu Yadetie, Astrid Laegreid and Inge Jonassen
XHM: A system for detection of potential cross hybridizations in DNA microarrays
BMC Bioinformatics 2004, 5:117 (27 August 2004)

Kane, M.D., Jatkoe, T.A., Stumpf, C.R., Lu, J., Thomas, J.D., and Madore, S.J. (2000).
Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays.
Nucleic Acids Research, 28(22):4552--4557.

Evertsz, E.M., Au-Young, J., et al. (2001).
Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays.
Biotechniques, 31(5):1182, 1184, 1186 passim.
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