SeqDown: An Efficient Sequence Retrieval Software and Comparative  Sequence Retrieval Analysis

Waqar  Hanif; Hijab  Fatima; Muhammad  Qasim; Rana Muhammad  Atif; Muhammad  Rizwan  Javed

doi:10.32350/cto.11.03

Waqar Hanif Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan; Research Center for Modelling and Simulation, National University of Science and Technology (NUST), Islamabad, Pakistan
Hijab Fatima Research Center for Modelling and Simulation, National University of Science and Technology (NUST), Islamabad, Pakistan
Muhammad Qasim Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
Rana Muhammad Atif Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
Muhammad Rizwan Javed Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan

DOI: https://doi.org/10.32350/cto.11.03

Keywords: bioinformatics, biological database, genbank, seqdown, sequence retrieval

Abstract

Abstract Views: 257

For any sequence analysis procedure, a single or multiple sequence must be retrieved, stored, organized. One of the most common public databases used for biological sequence retrieval is GenBank which is a comprehensive public database of nucleotide sequences. However, as the length of the sequence to be retrieved increases such as a chromosome, entire genome, scaffold, etc., the elapsed time to download the file gets even elongated due to slower bandwidth to download/retrieve the sequence.^[⁸^] In most cases, during sequence analysis, the researcher requires messenger RNA (mRNA), RNA, DNA, protein sequences of the same sequence-of-interest to work with, which consumes a substantial amount of the researcher in finding and retrieving the sequence files. An access to GenBank through JAVA HTTPS protocols is established to request and receive the sequence files associated with the input accessions. SeqDown was shown to be much efficient in terms of retrieval time of the sequences as compared to the other internet browsers and was found to be 15.27% faster than Mozilla Firefox. SeqDown also provides the feature to retrieve coding DNA sequences & protein sequences present in a single chromosome. Sequence retrieval from the most biological databases don’t have proper naming of their files and the user has to deal with the redundantly named sequence files which leads to incorrect and time-consuming analysis and can be solved with SeqDown. SeqDown is available as a free-to-download software at https://bit.ly/3cUwchz

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