PMC:1524773 / 46879-48004 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1524773","sourcedb":"PMC","sourceid":"1524773","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1524773","text":"For the test of our algorithm on biological sequences three BLAST-derived data sets were chosen as follows: From a bacterial artificial chromosome (BAC) and fosmid library of the genome of Pristionchus pacificus [13] that contains 78690 sequences, we reconstructed a genetic element that we characterized as a transposon from the maT family (S. Steigele, unpublished). Experimental hybridisation assays proved that this transposon is highly repetitive in the Pristionchus pacificus genome (A. Breit, unpublished). A BLASTN search (E-value \u003c 10-6) of this transposon against all sequences of the BAC and fosmid library was conducted, resulting in 126 hits below the E-value threshold. We refer to this data set by PpmaT. Furthermore, two multi-domain proteins, both containing repeated domains, were subject to BLASTP searches (E-value \u003c 10-6) versus the UniProt database [11]. The protein SH3 and multiple ankyrin repeat domains protein 1, short Shank1, contains 7 ANK repeats, 1 PDZ domain, 1 SAM domain and 1 SH3 domain. The BLAST search resulted in 86 hits below the E-value threshold. We refer to this data set by Shank1.","tracks":[{"project":"2_test","denotations":[{"id":"16737529-12884007-1692872","span":{"begin":213,"end":215},"obj":"12884007"},{"id":"16737529-15608167-1692873","span":{"begin":872,"end":874},"obj":"15608167"}],"attributes":[{"subj":"16737529-12884007-1692872","pred":"source","obj":"2_test"},{"subj":"16737529-15608167-1692873","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ece393","default":true}]}]}}