The following happened after many successful connections and queries to BioMart. Please, let me know whether the R script that implements such queries is of any help and I will attach the crucial lines of it. Thank you. Regards, Maura OPEN NEW CONNECTION ON FILE: hsa-miR-34b_V_MirBase_FastaFiles.txt **** WRITE 3UTR SEQUENCE TO FILE: hsa-miR- 34b_V_MirBase_FastaFiles.txt **** Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id", "refseq_dna", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_56: DBI connect('database=ensembl_mart_ 56;host=martdb.ensembl.org;port=5316','anonymous',...) failed: Lost connection to MySQL server at 'reading authorization packet', system error: 0 at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] microRNA_1.2.0 Rlibstree_0.3-2 gdata_2.4.2 CORNA_1.2 [5] XML_2.5-1 GEOquery_2.8.0 RCurl_0.98-1 bitops_1.0-4.1 [9] Biostrings_2.12.7 IRanges_1.2.3 biomaRt_2.0.0 Biobase_2.4.1 [13] JGR_1.6-7 iplots_1.1-3 JavaGD_0.5-2 rJava_0.6-3 loaded via a namespace (and not attached): [1] gtools_2.6.1 tutti i telefonini TIM! [[alternative HTML version deleted]]