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Pipeline publication

[…] dized to the chromosomes by standard procedures [] and then chromosomes were washed in 0.2XSSC, counterstained with YOYO-1 and mounted in DABCO []. Fluorescent signals were detected using a Bio-Rad MRC 1024 Scanning Confocal System (Bio-Rad Laboratories, Hercules, CA, USA)., The genomic sequences of A. gambiae scaffolds were downloaded from the VectorBase website []. For the estimation of gene density in scaffolds, 12,600 assembled expressed sequence tags from a Normalized Head library, Normalized Fat Body library and a pooled library were placed on scaffolds using BLAST, requiring an E value of <10-20. For the analysis of the simple repeat content with sizes smaller then 200 bp, we used Tandem Repeats Finder []. The percentage of sequences corresponding to the known transposable elements was found using the RepeatMasker program []. Two custom databases were used for the search: the database of the A. gambiae transposable elements (Maria Sharakhova and Frank Collins, unpublished data) and the database of natural transposable element sequences identified in D. melanogaster by M Ashburner et al. []., Scaffolds containing Y chromosome-specific satellite DNA families were regarded as Y-linked. They were identified using randomly selected monomer sequence of each of the four Y-specific satellite DNA families [] as a query in local BLASTN searches against the A. gambiae genome database., To identify BAC clones spanning gaps, BLASTN was utilized. A. gambiae BESs that demonstrated significant similarity (E < 10-50) to scaffolds on either side of gaps were selected. From this pool, BACs were identified as crossing gaps if paired BESs fulfilled the following criteria: matching the A. gambiae genomic sequence with an E value of <10-75, having the appropriate relative orientation, and preferably not being repeated on the scaffolds. The sequence length between the BES and the gap was then determined to identify the shortest BAC that crossed the gap, if more than one was identified, using the VectorBase genome viewer., To detect polymorphic scaffolds in the A. gambiae genome, unmapped scaffolds greater than 15 kbp […]

Pipeline specifications

Software tools TRF, RepeatMasker, BLASTN
Organisms Anopheles gambiae, Anopheles gambiae str. PEST
Diseases Malaria