Biopython/C2/Blast/Khasi

Time	Narration
00:01	Ngi pdiang sngewbha ia phi sha kane ka tutorial shaphang u BLAST da kaba pyndonkam ki tools u Biopython
00:06	Ha kane ka jinghikai , ngin sa nang kumno ban: run "BLAST" na ka bynta ka query sequence da kaba pyndonkam ki tools u Biopython.
00:13	Bad, parse ia u BLAST output ban tip kham bniah .
00:17	Ban sngewthuh ia kane ka tutorial, phi dei ban long kiba shemphang ha ka undergraduate Biochemistry lane Bioinformatics.
00:24	Bad ka basic Python programming.
00:27	Pyndonkam da ka Python tutorials na ka link ba ai harum.
00:31	Ban record ia kane ka tutorial, nga pyndonkam da ka: * Ubuntu Operating System version 14.10
00:37	Python version 2.7.8
00:41	Ipython interpretor version 2.3.0
00:46	Biopython version 1.64 bad ka internet ba trei kam.
00:52	BLAST ka dei ka acronym jong ka Basic Local Alignment Search Tool.
00:57	Ka dei ka algorithm ban pyniapher ki sequence information.
01:02	Kane ka program ka pyniapher ia ki nucleotide lane protein sequences sha ki sequences ha ki databases bad khein ia ka statistical significance jong ki matches .
01:14	Ki don artylli ki rukom ban run ia ka BLAST:
01:17	Ka Local BLAST ha ka machine jong phi lane run BLAST lyngba ka Internet jong ka NCBI servers.
01:24	Ki don ar tylli ki rukom ban pyndonkam ia ka BLAST ha ka Biopython
01:28	Nyngkong, run BLAST na ka bynta ka query sequence jong phi bad phin sa ioh output.
01:33	Ba ar, parse ka BLAST output na ka bynta ka jingkdew ba kham bniah hadien.
01:38	Ngin sa plie ia ka terminal bad run BLAST na ka bynta ka nucleotide sequence.
01:43	Plie ia ka terminal da kaba nion sah ia Ctrl, Alt bad T keys.
01:48	Ha ka prompt, type: ipython bad nion Enter.
01:52	Ha kane ka tutorial, ngan sa pyni kumno ban run ia ka BLAST lyngba ka internet da kaba pyndonkam da ka NCBI BLAST service.
02:01	Type kumne harum ha ka prompt: from Bio.Blast Import NCBIWWW Nion Enter.
02:14	Hadien , ban run ia u BLAST lyngba ka internet, type ia kaba bud ha ka prompt.result= NCBIWWW.qblast("blastn","nt","186429".
02:20	Ngin pyndonkam da ka qblast function ha ka NCBIWWW module.
02:25	qblast function ka shim lai tylli ki arguments:
02:29	Ka argument ba nyngkong ka dei ka blast program ba pyndonkam haba wad.
02:33	Ba ar, ka pyntikna ia ka databases ban wad pyrshah.
02:38	Ka argument ba lai ka dei ka query sequence. jong phi
02:43	Ka input jong ka query sequence ka lah ban dei ha ka rukon jong ka GI number lane ka FASTA file. Lane, ka lah ban dei ka sequence record object.
02:53	Na ka bynta kane ka jingpyni, nga pyndonkam ia ka GI number na ka bynta ka nucleotide sequence.
02:58	Ka GI number ka dei na ka bynta ka nucleotide sequence jong ka insulin
03:03	Ka qblast function ka shim ruh ia kiwei ki jait option arguments .
03:09	Kine ki arguments ki long kiba syrïem ha ki parameters bapher bapher ba phi lah ban buh ha ka BLAST web page.
03:15	Ka qblast function kan pynphai ia ka BLAST results ha ka xml format.
03:20	To ngin ia phai biang sha ka terminal.
03:22	Ngi hap ban pyndonkam da ka Blast program, ba tikna.
03:25	ka shong ruh lada ka query sequence jong ngi ka dei ka nucleotide lane protein sequence.
03:30	Katba ka query jong ngi ka dei ka nucleotide, ngin pyndonkam ka blastn program bad "nt" jong ka nucleotide database.
03:39	Ki jingtip ba kham bniah jong kine lah ban ioh na NCBI BLAST webpage.
03:45	Ia ka blast output la buh ha ka variable result, ha ka rukom jong ka xml file.
03:51	Nion Enter.
03:53	Ka shong ha ka jingstet jong ka internet jong ngi ban pyndep ia ka jingwad jong ka BLAST
03:59	Ka long ruh kaba donkam ban save ia ka xml file ha ka disk shuwa ban iaid shakhmat.
04:05	Type ia ki line ba bud bansave iaka xml file.
04:09	Kine ki lines jong ki code kin sa save ia ka jingwad kum blast.xml ha ka home folder.
04:18	Phai sha ka home folder jong ngi bad wad ia ka file.
04:21	Click ha ka file bad check ia ka contents (jingdon) jong ka file.
04:30	Pyndonkam ia u code ba pyni ha kane ka text file, lada phi kwah ban pyndonkam ia u FASTA file kum u query.
04:36	Hangne u don u code, lada phi kwah ban pyndonkam ia ka sequence record object na ka FASTA file kum ka query.
04:42	To ngin ia phai biang sha ka terminal.
04:44	Ka bynta ba bud ka dei ban parse ia ka file sha ka extract data.
04:48	Ka bynta ba nyngkong jong ka parsing ka dei ban plie ia ka xml file na ka bynta ka input.
04:53	Type kumne harum ha ka prompt. Nion Enter.
04:57	Hadien , import ia ka module NCBIXML na "Bio.Blast" package.
05:05	Nion Enter.
05:07	Type ia ki lines ba bud sha ka parse ia ka Blast output.
05:11	Ka BLAST record ka don ia baroh ki jingpyntip ba phi kwah ban extract na ka BLAST output.
05:18	To ngin ia print khyndiat ia ki jingpyntip shaphang baroh ki hits ha ki blast report jong ngi kiba kham heh ban ha ki jaka ba ki mih.
05:27	Type ia u code harum.
05:30	Khnang ba ka match kan long kaba tikna, peit ba u score u dei ban rit ia ka 0.01.
05:37	Na ka bynta uwei pa uwei u hsp, kata ka mut, ki shijur ba heh score, ngi ioh ia ka title, length, hsp score, gaps bad expect value.
05:49	Ngin ia print ruh ia u strings uba don ia ka query, ka database sequence ba la pynbeit bad u string ba pyntikna ia ka jingiadei bad jingbymiadei ki positions.
06:02	Nion ia u Enter key arsien ban ioh ia ka output.
06:05	Peit ia ka jingmih
06:09	Na ka bynta kawei pa kawei ka alignment, ngi don length, score, gaps, evalue bad strings.
06:16	Phi lah ban ioh ia ki jingpyntip ba donkam da kaba pyndonkam kiwei ki functions, ki ba don ha Bio.Blast package.
06:24	Ngi lah poi sha kaba kut jong kane ka tutorial.
06:26	To ngin ia khmih ia kaei kaba ngi lah leh haneng . Ha kane ka tutorial, ngi lah tip kumno ban run ia ka BLAST na ka bynta ka query nucleotide sequence da kaba pyndonkam da u GI number.
06:36	Bad, ban parse ia u BLAST output da kaba pyndonkam da ka Bio.Blast.Record module.
06:43	Na ka bynta ka assignment, run BLAST Search na ka bynta ka protein sequence kaba ngi kwah.
06:50	Save ia ka output file bad parse ia ka data kaba don ha ka file.
06:55	Ka assignment ba lah dep jong phi ka dei ban don ia ki lines ba don code , kumba lah pyni ha kane ka file.
07:01	Peit ia u code. Katba ka query jong ngi ka dei protein sequence, ngi lah pyndonkam blastp program and "nr", kata ka mut, ka protein database kaba donkam na ka bynta ka BLAST search.
07:16	Ka video kaba don ha ka link ba bud ka batai shai shaphang ka Spoken Tutorial project.
07:20	Sngewbha download bad peit ia ka.
07:22	Ka Spoken Tutorial Project team ka ju pynlong ia ki workshops bad ai ruh ki certificates ia kito kiba pass ia ka online test.
07:30	Na ka bynta ka jingtip ba kham bniah, sngewbha thoh sha ngi.
07:33	Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India.
07:40	Ki jingtip ba kham pura ia kane ka mission lah ban ioh na link harum.
07:45	Ia kane ka script la pynkylla sha ka ktien khasi da u Yuwanki Kharlukhi bad ma Nga u Hezekiah Lyngdoh ngan pynkut noh. Khublei shibun .

Contributors and Content Editors

Hezekiah2016