Where or How can I find contigs? I am trying to learn Bioinformatics and I want to make a reference-based gene search. I also want to align contigs with a given reference sequence. From NCBI other databases I can find only reads and complete genome sequences. Please tell me how can I find contig sequences of a species?
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Most of the reference genomes on NCBI are made of contigs or scaffolds (which is just a fancy name for contigs glued together by a bunch of unknown nucleotides). Hence, by download the whole genome, you also download all the contigs.
If you search for a specific contig (presumably a known locus) of a specific species, you can search NCBI for the species name + locus / scaffold / contig name and if it was sequenced it will pop up in the "genes" section of NCBI. For example, here is a search for Pan troglodites contig NC_036898.1 (I typed literally Pan troglodites NC_036898.1 in the search bar). You can even just type a species name, and click on "genes" and see loads of all the individual contigs sequenced.
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There is a bunch of ways to generate something we could call contig. However, usually what we mean is "continuous sequence assembled from sequencing reads" and it's generated from whole-genome sequencing reads. We sequence a genome, assemble the reads and what we get is a set of contigs as a representation of a haploid reference genome. Some of them will be short fragments of nucleotides with unknown functions, some of them can be long and contain hundreds of genes. The important part is that it's a continuous sequence.
With a bit more relaxed definition of "contig", we could also accept as contigs outputs of targeted sequencing (including old-fashioned sanger). It's a continuous stretch of nucleotides, usually bordered by a pair of primers. I am not 100% sure, but my best guess that most of the "gene" sequences in NCBI will be sanger-based (but I should disclaim I never investigated too much where all the NCBI sequences come from).
answered May 28, 2021 at 10:18
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$\begingroup$ This helps thank you but how can i find the contigs/scaffolds before they were assembled to a reference sequence/whole genome. In the genes section of NCBI, I can find list of annotated genes with their sequence, i thought contigs/scaffolds are longer than one gene and contain other features? $\endgroup$– abelfitCommented May 28, 2021 at 13:12
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$\begingroup$ I tried to clarify the answer to address your questions. Is it better now? $\endgroup$ Commented May 28, 2021 at 14:16