We have sequenced a transcriptome of a species who does not have a sequenced genome, using 454 and our initial goal is to find a set of ESTs that represent genes. The 454 reads were assembled using Newbler 2.5 and the initial assembly gave ~26000 isotigs and 18,000. Contigs. After talking to the several people, I used CD-Hits program to combine the isotigs, contigs and singltons that were not assembled. After combining these sequences, I got ~4000 isotigs, ~17,000 contigs and ~30, 000 Singlton that were not assembled. Is this the correct way to do this? I couldn’t find any publication that has mentioned this method.
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by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
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04-04-2024, 04:25 PM -
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by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
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