Scan Prosite Database with Bio.ExPASy.ScanProsite.scan()

Q

How to Scan Prosite Database with Bio.ExPASy.ScanProsite.scan() function?

✍: FYIcenter.com

A

Bio.ExPASy.ScanProsite.scan() function allows to scan the Prosite database with a given sequence.

Here is an example on how to Scan Prosite Database.

fyicenter$ python 
>>> from Bio.ExPASy import ScanProsite

>>> sequence = (
...   "MEHKEVVLLLLLFLKSGQGEPLDDYVNTQGASLFSVTKKQLGAGSIEECAAKCEEDEEFT"
...   "CRAFQYHSKEQQCVIMAENRKSSIIIRMRDVVLFEKKVYLSECKTGNGKNYRGTMSKTKN"
... )
>>> handle = ScanProsite.scan(seq=sequence)

>>> result = ScanProsite.read(handle)
>>> len(result)
1

>>> result[0]
{'sequence_ac': 'USERSEQ1', 'start': 16, 'stop': 98, 'signature_ac': 'PS50948', 'score': '8.873', 'level': '0'}

⇒ Read Sequence Alignments with Bio.AlignIO

⇐ Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw()

⇑ Biopython - Tools for Biological Computation

⇑⇑ OBF (Open Bioinformatics Foundation) Tools

2023-09-05, 1664🔥, 0💬

Fetch Sequences from NCBI with Bio.Entrez.efetch()
How to Fetch Sequences from NCBI with the Bio.Entrez.efetch() function? Bio.Entrez.efetch() function allows you to fetch DNA or protein sequences from NCBI databases: PubMed, GenBank, GEO, and many others. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. Here is an example on how to... 2023-08-25, 1160🔥, 0💬

Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()
How to Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()? The function qblast() in the Bio.Blast.NCBIWWW module allows you to call the online version of BLAST to fetch DNA or protein sequences from https://blast.ncbi.nlm.nih.gov /Blast.cgi.Currently the qblast() function only works with 5 BL... 2023-05-09, 1145🔥, 0💬

Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw()
How to Fetch Sequences from SwissProt with Bio.ExPASy.get_sprot_raw() function? SwissProt with Bio.ExPASy.get_sprot_raw() function allows you to fetch protein sequences from SwissProt database. Here is an example on how to Fetch Sequences from SwissProt. fyicenter$ python >>> fr... 2023-09-10, 1067🔥, 0💬

Read Sequence Alignments with Bio.AlignIO
How to Read Sequence Alignments with Bio.AlignIO package? Bio.AlignIO module allows you to read and write Sequence Alignments as MultipleSeqAlignment objects. Enter the following sequence alignment file, PF05371_seed.faa, in FASTA format. >COATB_BPIKE/30-81 AEPNAATNYATEAMDSLKTQAIDLISQTWP VVTTV... 2023-09-05, 1046🔥, 0💬

Parse PDB Entry with Bio.PDB.MMCIFParser.parser Module
How to Parse PDB Entry with Bio.PDB.MMCIFParser.parser.get _structure()function? Bio.PDB.MMCIFParser.parser.get _structure()function allows you to parse and any PDB (Protein Database) data files. 1. Download a PDB file in PDB format. fyicenter$ curl http://files.rcsb.org/view/1fa t.pdb> 1fat.... 2023-05-09, 1001🔥, 0💬

Search History with Bio.Entrez for Subsequent Calls
How to Use Search History with Bio.Entrez for Subsequent Calls? If use Bio.Entrez.esearch() and found a large number of matches, you can use the history feature to retrieve matched records in multiple sequence Bio.Entrez.efetch() calls. 1. Turn on the history feature in the esearch() call with the u... 2023-09-10, 996🔥, 0💬

Calculate Substitutions in Alignments
How to Calculate Substitutions in Sequence Alignments? The substitutions property of an alignment reports how often letters in the alignment are substituted for each other. This is calculated by taking all pairs of rows in the alignment, counting the number of times two letters are aligned to each o... 2023-08-03, 995🔥, 0💬

Use Bio.SearchIO Module to Parse BLAST XML Result
How to Use Bio.SearchIO Module to Parse BLAST XML Result? The Bio.SearchIO module allows to parse sequence search result from different result format. 1. Try the following code to query the "nt" database under the "blastn" program with a given DNA sequence, which is reverse translated from a protein... 2023-05-09, 988🔥, 0💬

All rights in the contents of this web site are reserved by the individual author. fyicenter.com does not guarantee the truthfulness, accuracy, or reliability of any contents.