VascoElbrecht's video: Searching and verifying NCBI SRA sequences suited for mitogenome assembly Part 2

We want to assemble a mitochondrial genome using SRA next generation sequencing data freely available on NCBI. As an target group we have chosen Stoneflys (Plecoptera), and we have to check which mitogenomes are already available and which SRA libraries could be suitable for mitogenome assembly. Table of contents: 0:16 Search for plecopteran NGS datasets in the SRA, which can be used for mitogenome assembly and which are not suitable? http://www.ncbi.nlm.nih.gov/sra/?term=plecoptera 2:33 We have found a potential Illumina data set (Species: Mesocapnia arizonensis, Capniidae), but there is an potential mistake in the meta data of the entry which we should check later on. http://www.ncbi.nlm.nih.gov/sra/SRX450973 3:23 Check if there is an mitochondrial genome available for Mesocapnia and download available plecopteran genomes. http://www.ncbi.nlm.nih.gov/nuccore/?term=Plecoptera+mitochondrial+genome 5:06 Figure out who has uploaded the NGS data in the SRA and se if there are publications associated with the data. In this case the data was used for microsatellite development and is published here: http://dx.plos.org/10.1371/journal.pone.0081853 Lance et al. 2013 32 species validation of a new Illumina paired-end approach for the development of microsatellites 7:42 Search NCBI if there are mitochondrial sequences available for Mesocapnia. http://www.ncbi.nlm.nih.gov/nuccore/?term=Mesocapnia 9:28 Take a closer look at the SRA sequence quality http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1145747 9:40 Blast the Mesocapnia COII gene (EF622986.1) against the SRA sequences (SRR1145747) to verify that they are indeed belonging to the Genus Mesocapnia. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&DB_GROUP=Exp Next video: Downloading the SRA reads and converting them to the fastq sequence format. https://www.youtube.com/watch?v=NSIkUHKRPpo