Biopython/C2/Blast/Khasi

Time	Narration
00:01	Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka BLAST da kaba pyndonkam ki tools u Biopython
00:06	Ha kane ka tutorial, ngin pule 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 wad bniah shuh shuh.
00:17	Ban bud ia kane ka tutorial, phi dei ban tip bha iaka undergraduate Biochemistry lane Bioinformatics.
00:24	Bad ka basic Python programming.
00:27	Peit ia 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 ktien lyngkot jong ka Basic Local Alignment Search Tool.
00:57	Ka dei ka algorithm ban ia nujor ki sequence information.
01:02	Kane ka program ka ia nujor ia ki nucleotide lane protein sequences sha ki sequences ha ki databases bad khein ia ka statistical significance jong ki jingiahap.
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 lyngba ka NCBI servers.
01:24	Ki don ar tylli ki rukom ban run ia ka BLAST ha ka Biopython
01:28	Nyngkong, run ia ka BLAST na ka bynta ka query sequence jong phi bad pynioh katto katne ka output.
01:33	Ba ar, parse ka BLAST output na ka bynta ka jingwad ba kham bniah hadien.
01:38	Ngin plie ia ka terminal bad run BLAST na ka bynta ka nucleotide sequence.
01:43	Plie ia ka terminal da kaba nion lang 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 ka NCBI BLAST service.
02:01	Type kumne harum ha ka prompt: from Bio.Blast Import NCBIWWW Nion Enter.
02:14	Ka ba bud, ban run ia u BLAST lyngba ka internet, type ia kaba harum 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 naka bynta ban wad.
02:33	Ba ar, pyntikna ia ka databases ban wad pyrshah.
02:38	Ka argument ba lai ka dei ka query sequence. jong phi
02:43	Ka input na ka bynta ka query sequence ka lah ban long ha ka rukom jong ka GI number lane ka FASTA file. Lane, ka lah ruh ban long 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 argument ba bun.
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	Phai biang sha ka terminal.
03:22	Ngi dei 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	Namar ka query jong ngi ka dei ka nucleotide, ngin pyndonkam ka blastn program bad "nt" ka thew ia ka nucleotide database.
03:39	Ki jingtip ba kham bniahsShaphang kine ki don haka 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 phi, ka lah ban shim katto katne minute ban pyndep ïaka BLAST search.
03:59	Ka long kaba kongsan ban save ia ka xml file ha ka disk shuwa ban iaid shakhmat.
04:05	Type ia ki line harum 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 phi bad wad ia ka file.
04:21	Click ha ka file bad check ia ka 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 ban extract data.
04:48	Ka synjam 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	Kaba bud, import ia ka module NCBIXML na "Bio.Blast" package.
05:05	Nion Enter.
05:07	Type ia ki lines harum ban 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	Na bynta ka match ba kan long kaba tikna, ka expect score kam dei ban duna 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	Khmih thuh ia ka output.
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 batai lyngkot. Ha kane ka tutorial, ngi la pule 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 phi 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 lain jong ki code ba harum, kumba lah pyni ha kane ka file.
07:01	Khmih thuh ia u code. Namar ka query jong ngi ka dei protein sequence, ngi lah pyndonkam blastp program bad "nr", kata ka mut, ka protein database ka bym da donkam na ka bynta ka BLAST search.
07:16	Ka video kaba don ha ka link harum ka batai lyngkot 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	Ban tip kham bniah, sngewbha thoh sha ngi.
07:33	Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Sorkar India.
07:40	Khambun ki jingtip halor kane ka mission ka don ha ka link harum.
07:45	ïa kane ka script la pynkylla sha ka Ktien Khasi da u Yuwanki Kharlukhi na Shillong, bad ma nga u Hezekiah Lyngdoh ngan pynkut noh. khublei ba phi la ïasnoh lang..

Contributors and Content Editors

Hezekiah2016