Question

How to download protein sequences

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3.1 years ago

Nelo ▴ 20

Hi

I need to download Aquaporin protein fasta sequences of Melon plant species. From the paper it was mentioned that the number of AQP protein in melon is 31 with given Gene ID like 103501427, 103482758, 103491188. If i search in NCBI using this ID, different result popup instead of AQP while in Uniprot, AQP of melon is being displayed.

Is there any way to download all this 31 AQP protein sequences using any tools or NCBI entrez or any other program without using this Gene ID "OR" downloading without the help of accession number ??

Any hints Tnkq

plant fasta AQP • 1.2k views

ADD COMMENT • link 3.1 years ago by Nelo ▴ 20

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while in Uniprot, AQP of melon is being displayed

So those are UniProt Id's and not NCBI ID's then?

ADD REPLY • link 3.1 years ago by GenoMax 146k

score 3 · Accepted Answer · 2021-09-15

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3.1 years ago

GenoMax 146k

Using Entrezdirect: (sequences truncated for space, there are a total of 94).

$ esearch -db protein -query "aquaporin AND Cucumis melo [orgn]" | efetch -format fasta 

>NP_001380707.1 aquaporin PIP1-1 [Cucumis melo]
MEGKEEDVRLGANKFNERQPIGTAAQSQDDAKDYKEPPPAPLFEPEELTSWSFYRAGIAEFFATFLFLYI

>NP_001380722.1 aquaporin XIP1-1 [Cucumis melo]
MAQEEFALPLEEEEGRSFDEQTSSSSSFLSRFLIYIGAHELFSQEMWKAAMTELVATALLIFCLTTSIVS

>NP_001380721.1 aquaporin NIP5-2 [Cucumis melo]
MAQFEIVRVDSPKRSQILDVSLTRKVAAEFVGTFILIFGATAAPIVNQKYNSPMSLIGNAACSGIAVMIV

>NP_001380720.1 aquaporin NIP4-1 [Cucumis melo]
MATKIDGIEDEEISKLEEGTVVSAIARLCPSNSVVIIQKVIAELIGTYFVIFSGCGAVAVNKIYGSVTFP

ADD COMMENT • link 3.1 years ago by GenoMax 146k

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Thank you so much.

This command is actually retrieving all the AQPs including the isoforms of Melon species. I got 94 sequences, but still it is ok for me. Rest I will manually filter the sequences .

Tnks a lot!!!

ADD REPLY • link 3.1 years ago by Nelo ▴ 20

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If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
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ADD REPLY • link 3.1 years ago by GenoMax 146k

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okie

Done

ADD REPLY • link 3.1 years ago by Nelo ▴ 20